data-raw/03-create_internal_rda.R
In sartorlab/methylSig: MethylSig: Differential Methylation Testing for WGBS and RRBS Data
library(bsseq)
library(DelayedArray)
library(GenomicRanges)
################################################################################
# Use for tile_by_regions() tests
# Use for filter_loci_by_location() tests
#----[---------]---------[--------------]----[---------]--------------[---------]
gr_tiles1 = GRanges(
seqnames = c('chr1','chr1','chr1','chr1'),
ranges = IRanges(
start = c(5,25,45,70),
end = c(15,40,55,80)
)
)
# Use for tiling tests
#----[------------------------]----[----------------------------------]----[----]
gr_tiles2 = GRanges(
seqnames = c('chr1','chr1','chr1'),
ranges = IRanges(
start = c(5,35,75),
end = c(30,70,80)
)
)
# Use for tiling tests
# Use for filter_loci_by_location() tests (expect an error from removing all)
#----[--------------------------------------------------------------------------]
gr_tiles3 = GRanges(
seqnames = c('chr1'),
ranges = IRanges(
start = c(5),
end = c(80)
)
)
# Use for tiling tests
# Use for filter_loci_by_location() tests
#----[--------------]------------------------------------------------------------
gr_tiles4 = GRanges(
seqnames = c('chr1'),
ranges = IRanges(
start = c(5),
end = c(20)
)
)
# Use for tiling tests
# Use for filter_loci_by_location() tests (expect nothing filtered)
#----[---]-----------------------------------------------------------------------
gr_tiles5 = GRanges(
seqnames = c('chr1'),
ranges = IRanges(
start = c(5),
end = c(9)
)
)
#[-----------------------][-----------------------][-----------------------][-----------------------][]
seqlengths = c('chr1' = 101)
win25_stranded_gr = GenomicRanges::tileGenome(
seqlengths = seqlengths,
tilewidth = 25,
cut.last.tile.in.chrom = TRUE)
#[-----------------------][-----------------------][-----------------------][-----------------------]
seqlengths = c('chr1' = 100)
win25_destranded_gr = GenomicRanges::tileGenome(
seqlengths = seqlengths,
tilewidth = 25,
cut.last.tile.in.chrom = TRUE)
#[-----------------------][-----------------------][---]
#[-----------------------][---]
seqlengths = c('chr1' = 55, 'chr2' = 35)
win25_multichrom_gr = GenomicRanges::tileGenome(
seqlengths = seqlengths,
tilewidth = 25,
cut.last.tile.in.chrom = TRUE)
################################################################################
# gr_tiles1
################################################################################
#----[---------]---------[--------------]----[---------]--------------[---------]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# test1 coverage
# 5 30 10 0 40 1000
# 5 70 20 0 1500
# test2 coverage
# 10 50 15 5 20 100
# 10 50 35 5 200
#----[---------]---------[--------------]----[---------]--------------[---------]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# tile_by_regions(bs = bsseq_stranded, gr = gr_tiles1) coverage
# 10 110 0 2500
# 20 115 10 300
stranded_cov1 = DelayedArray::DelayedArray(matrix(c(
10,110,0,2500,
20,115,10,300
), ncol = 2))
#----[---------]---------[--------------]----[---------]--------------[---------]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# test1 coverage
# 5 30 10 0 40 1000
# 5 70 20 0 1500
# test2 coverage
# 10 50 15 5 20 100
# 10 50 35 5 200
#----[---------]---------[--------------]----[---------]--------------[---------]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# filter_loci_by_location(bs = bsseq_stranded, gr = gr_tiles1) coverage
# 20 40
# 35 20
filter_cov1 = DelayedArray::DelayedArray(matrix(c(
20,40,
35,20
), ncol = 2))
#----[---------]---------[--------------]----[---------]--------------[---------]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# test1 methylation
# 4 0 9 0 35 900
# 4 5 19 0 1400
# test2 methylation
# 9 1 14 5 15 99
# 9 5 34 5 199
#----[---------]---------[--------------]----[---------]--------------[---------]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# tile_by_regions(bs = bsseq_stranded, gr = gr_tiles1) methylation
# 8 14 0 2300
# 18 20 10 298
stranded_meth1 = DelayedArray::DelayedArray(matrix(c(
8,14,0,2300,
18,20,10,298
), ncol = 2))
#----[---------]---------[--------------]----[---------]--------------[---------]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# test1 methylation
# 4 0 9 0 35 900
# 4 5 19 0 1400
# test2 methylation
# 9 1 14 5 15 99
# 9 5 34 5 199
#----[---------]---------[--------------]----[---------]--------------[---------]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# filter_loci_by_location(bs = bsseq_stranded, gr = gr_tiles1) methylation
# 19 35
# 34 15
filter_meth1 = DelayedArray::DelayedArray(matrix(c(
19,35,
34,15
), ncol = 2))
bsseq_stranded_tiled1 = BSseq(
gr = gr_tiles1,
Cov = stranded_cov1,
M = stranded_meth1,
pData = data.frame(row.names = c('test1','test2')),
sampleNames = c('test1','test2')
)
filter_loc_tiles1 = BSseq(
gr = granges(bsseq_stranded[c(6,9)]),
Cov = filter_cov1,
M = filter_meth1,
pData = data.frame(row.names = c('test1','test2')),
sampleNames = c('test1','test2')
)
########################################
#----[---------]---------[--------------]----[---------]--------------[---------]
#---------C--------------C--------------C---------C---------C--------------C-
# test1 coverage
# 10 100 30 0 40 2500
# test2 coverage
# 20 100 50 10 20 300
#----[---------]---------[--------------]----[---------]--------------[---------]
#---------C--------------C--------------C---------C---------C--------------C-
# tile_by_regions(bs = bsseq_destranded, gr = gr_tiles1) coverage
# 10 130 0 2500
# 20 150 10 300
destranded_cov1 = DelayedArray::DelayedArray(matrix(c(
10,130,0,2500,
20,150,10,300
), ncol = 2))
#----[---------]---------[--------------]----[---------]--------------[---------]
#---------C--------------C--------------C---------C---------C--------------C-
# test1 methylation
# 8 5 28 0 35 2300
# test2 methylation
# 18 6 48 10 15 298
#----[---------]---------[--------------]----[---------]--------------[---------]
#---------C--------------C--------------C---------C---------C--------------C-
# tile_by_regions(bs = bsseq_destranded, gr = gr_tiles1) methylation
# 8 14 0 2300
# 18 54 10 298
destranded_meth1 = DelayedArray::DelayedArray(matrix(c(
8,33,0,2300,
18,54,10,298
), ncol = 2))
bsseq_destranded_tiled1 = BSseq(
gr = gr_tiles1,
Cov = destranded_cov1,
M = destranded_meth1,
pData = data.frame(row.names = c('test3','test4')),
sampleNames = c('test3','test4')
)
################################################################################
# gr_tiles2
################################################################################
#----[------------------------]----[----------------------------------]----[----]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# test1 coverage
# 5 30 10 0 40 1000
# 5 70 20 0 1500
# test2 coverage
# 10 50 15 5 20 100
# 10 50 35 5 200
#----[------------------------]----[----------------------------------]----[----]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# tile_by_regions(bs = bsseq_stranded, gr = gr_tiles2) coverage
# 110 70 2500
# 120 80 300
stranded_cov2 = DelayedArray::DelayedArray(matrix(c(
110,70,2500,
120,80,300
), ncol = 2))
#----[------------------------]----[----------------------------------]----[----]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# test1 methylation
# 4 0 9 0 35 900
# 4 5 19 0 1400
# test2 methylation
# 9 1 14 5 15 99
# 9 5 34 5 199
#----[------------------------]----[----------------------------------]----[----]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# tile_by_regions(bs = bsseq_stranded, gr = gr_tiles2) methylation
# 13 63 2300
# 24 73 298
stranded_meth2 = DelayedArray::DelayedArray(matrix(c(
13,63,2300,
24,73,298
), ncol = 2))
bsseq_stranded_tiled2 = BSseq(
gr = gr_tiles2,
Cov = stranded_cov2,
M = stranded_meth2,
pData = data.frame(row.names = c('test1','test2')),
sampleNames = c('test1','test2')
)
########################################
#----[------------------------]----[----------------------------------]----[----]
#---------C--------------C--------------C---------C---------C--------------C-
# test1 coverage
# 10 100 30 0 40 2500
# test2 coverage
# 20 100 50 10 20 300
#----[------------------------]----[----------------------------------]----[----]
#---------C--------------C--------------C---------C---------C--------------C-
# tile_by_regions(bs = bsseq_destranded, gr = gr_tiles2) coverage
# 110 70 2500
# 120 80 300
destranded_cov2 = DelayedArray::DelayedArray(matrix(c(
110,70,2500,
120,80,300
), ncol = 2))
#----[------------------------]----[----------------------------------]----[----]
#---------C--------------C--------------C---------C---------C--------------C-
# test1 methylation
# 8 5 28 0 35 2300
# test2 methylation
# 18 6 48 10 15 298
#----[------------------------]----[----------------------------------]----[----]
#---------C--------------C--------------C---------C---------C--------------C-
# tile_by_regions(bs = bsseq_destranded, gr = gr_tiles2) methylation
# 13 63 2300
# 24 73 298
destranded_meth2 = DelayedArray::DelayedArray(matrix(c(
13,63,2300,
24,73,298
), ncol = 2))
bsseq_destranded_tiled2 = BSseq(
gr = gr_tiles2,
Cov = destranded_cov2,
M = destranded_meth2,
pData = data.frame(row.names = c('test3','test4')),
sampleNames = c('test3','test4')
)
################################################################################
# gr_tiles3
################################################################################
#----[--------------------------------------------------------------------------]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# test1 coverage
# 5 30 10 0 40 1000
# 5 70 20 0 1500
# test2 coverage
# 10 50 15 5 20 100
# 10 50 35 5 200
#----[--------------------------------------------------------------------------]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# tile_by_regions(bs = bsseq_stranded, gr = gr_tiles3) coverage
# 2680
# 500
stranded_cov3 = DelayedArray::DelayedArray(matrix(c(
2680,
500
), ncol = 2))
#----[--------------------------------------------------------------------------]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# test1 methylation
# 4 0 9 0 35 900
# 4 5 19 0 1400
# test2 methylation
# 9 1 14 5 15 99
# 9 5 34 5 199
#----[--------------------------------------------------------------------------]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# tile_by_regions(bs = bsseq_stranded, gr = gr_tiles3) methylation
# 2376
# 395
stranded_meth3 = DelayedArray::DelayedArray(matrix(c(
2376,
395
), ncol = 2))
bsseq_stranded_tiled3 = BSseq(
gr = gr_tiles3,
Cov = stranded_cov3,
M = stranded_meth3,
pData = data.frame(row.names = c('test1','test2')),
sampleNames = c('test1','test2')
)
########################################
#----[------------------------]----[----------------------------------]----[----]
#---------C--------------C--------------C---------C---------C--------------C-
# test1 coverage
# 10 100 30 0 40 2500
# test2 coverage
# 20 100 50 10 20 300
#----[------------------------]----[----------------------------------]----[----]
#---------C--------------C--------------C---------C---------C--------------C-
# tile_by_regions(bs = bsseq_destranded, gr = gr_tiles3) coverage
# 2680
# 500
destranded_cov3 = DelayedArray::DelayedArray(matrix(c(
2680,
500
), ncol = 2))
#----[------------------------]----[----------------------------------]----[----]
#---------C--------------C--------------C---------C---------C--------------C-
# test1 methylation
# 8 5 28 0 35 2300
# test2 methylation
# 18 6 48 10 15 298
#----[------------------------]----[----------------------------------]----[----]
#---------C--------------C--------------C---------C---------C--------------C-
# tile_by_regions(bs = bsseq_destranded, gr = gr_tiles3) methylation
# 2376
# 395
destranded_meth3 = DelayedArray::DelayedArray(matrix(c(
2376,
395
), ncol = 2))
bsseq_destranded_tiled3 = BSseq(
gr = gr_tiles3,
Cov = destranded_cov3,
M = destranded_meth3,
pData = data.frame(row.names = c('test3','test4')),
sampleNames = c('test3','test4')
)
################################################################################
# gr_tiles4
################################################################################
#----[--------------]------------------------------------------------------------
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# test1 coverage
# 5 30 10 0 40 1000
# 5 70 20 0 1500
# test2 coverage
# 10 50 15 5 20 100
# 10 50 35 5 200
#----[--------------]------------------------------------------------------------
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# tile_by_regions(bs = bsseq_stranded, gr = gr_tiles4) coverage
# 10
# 20
stranded_cov4 = DelayedArray::DelayedArray(matrix(c(
10,
20
), ncol = 2))
filter_cov4 = DelayedArray::DelayedArray(matrix(c(
30,70,10,20,0,0,40,1000,1500,
50,50,15,35,5,5,20,100,200
), ncol = 2))
#----[--------------]------------------------------------------------------------
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# test1 methylation
# 4 0 9 0 35 900
# 4 5 19 0 1400
# test2 methylation
# 9 1 14 5 15 99
# 9 5 34 5 199
#----[--------------]------------------------------------------------------------
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# tile_by_regions(bs = bsseq_stranded, gr = gr_tiles4) methylation
# 8
# 18
stranded_meth4 = DelayedArray::DelayedArray(matrix(c(
8,
18
), ncol = 2))
filter_meth4 = DelayedArray::DelayedArray(matrix(c(
0,5,9,19,0,0,35,900,1400,
1,5,14,34,5,5,15,99,199
), ncol = 2))
bsseq_stranded_tiled4 = BSseq(
gr = gr_tiles4,
Cov = stranded_cov4,
M = stranded_meth4,
pData = data.frame(row.names = c('test1','test2')),
sampleNames = c('test1','test2')
)
filter_loc_tiles4 = BSseq(
gr = granges(bsseq_stranded[-c(1,2)]),
Cov = filter_cov4,
M = filter_meth4,
pData = data.frame(row.names = c('test1','test2')),
sampleNames = c('test1','test2')
)
########################################
#----[--------------]------------------------------------------------------------
#---------C--------------C--------------C---------C---------C--------------C-
# test1 coverage
# 10 100 30 0 40 2500
# test2 coverage
# 20 100 50 10 20 300
#----[--------------]------------------------------------------------------------
#---------C--------------C--------------C---------C---------C--------------C-
# tile_by_regions(bs = bsseq_destranded, gr = gr_tiles4) coverage
# 10
# 20
destranded_cov4 = DelayedArray::DelayedArray(matrix(c(
10,
20
), ncol = 2))
#----[--------------]------------------------------------------------------------
#---------C--------------C--------------C---------C---------C--------------C-
# test1 methylation
# 8 5 28 0 35 2300
# test2 methylation
# 18 6 48 10 15 298
#----[--------------]------------------------------------------------------------
#---------C--------------C--------------C---------C---------C--------------C-
# tile_by_regions(bs = bsseq_destranded, gr = gr_tiles4) methylation
# 8
# 18
destranded_meth4 = DelayedArray::DelayedArray(matrix(c(
8,
18
), ncol = 2))
bsseq_destranded_tiled4 = BSseq(
gr = gr_tiles4,
Cov = destranded_cov4,
M = destranded_meth4,
pData = data.frame(row.names = c('test3','test4')),
sampleNames = c('test3','test4')
)
################################################################################
# gr_tiles5
################################################################################
#----[---]-----------------------------------------------------------------------
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# test1 coverage
# 5 30 10 0 40 1000
# 5 70 20 0 1500
# test2 coverage
# 10 50 15 5 20 100
# 10 50 35 5 200
#----[---]-----------------------------------------------------------------------
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# tile_by_regions(bs = bsseq_stranded, gr = gr_tiles5) coverage
# 0
# 0
stranded_cov5 = DelayedArray::DelayedArray(matrix(c(
0,
0
), ncol = 2))
#----[---]-----------------------------------------------------------------------
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# test1 methylation
# 4 0 9 0 35 900
# 4 5 19 0 1400
# test2 methylation
# 9 1 14 5 15 99
# 9 5 34 5 199
#----[---]-----------------------------------------------------------------------
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# tile_by_regions(bs = bsseq_stranded, gr = gr_tiles5) methylation
# 0
# 0
stranded_meth5 = DelayedArray::DelayedArray(matrix(c(
0,
0
), ncol = 2))
bsseq_stranded_tiled5 = BSseq(
gr = gr_tiles5,
Cov = stranded_cov5,
M = stranded_meth5,
pData = data.frame(row.names = c('test1','test2')),
sampleNames = c('test1','test2')
)
########################################
#----[---]-----------------------------------------------------------------------
#---------C--------------C--------------C---------C---------C--------------C-
# test1 coverage
# 10 100 30 0 40 2500
# test2 coverage
# 20 100 50 10 20 300
#----[---]-----------------------------------------------------------------------
#---------C--------------C--------------C---------C---------C--------------C-
# tile_by_regions(bs = bsseq_destranded, gr = gr_tiles5) coverage
# 0
# 0
destranded_cov5 = DelayedArray::DelayedArray(matrix(c(
0,
0
), ncol = 2))
#----[---]-----------------------------------------------------------------------
#---------C--------------C--------------C---------C---------C--------------C-
# test1 methylation
# 8 5 28 0 35 2300
# test2 methylation
# 18 6 48 10 15 298
#----[---]-----------------------------------------------------------------------
#---------C--------------C--------------C---------C---------C--------------C-
# tile_by_regions(bs = bsseq_destranded, gr = gr_tiles5) methylation
# 0
# 0
destranded_meth5 = DelayedArray::DelayedArray(matrix(c(
0,
0
), ncol = 2))
bsseq_destranded_tiled5 = BSseq(
gr = gr_tiles5,
Cov = destranded_cov5,
M = destranded_meth5,
pData = data.frame(row.names = c('test3','test4')),
sampleNames = c('test3','test4')
)
filter_loc_tiles5 = bsseq_stranded
################################################################################
# win25_gr
################################################################################
#[-----------------------][-----------------------][-----------------------][-----------------------][]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# test1 coverage
# 5 30 10 0 40 1000
# 5 70 20 0 1500
# test2 coverage
# 10 50 15 5 20 100
# 10 50 35 5 200
#[-----------------------][-----------------------][-----------------------][-----------------------][]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# tile_by_windows(bs = bsseq_stranded, win_size = 25) coverage
# 40 100 1040 1500 0
# 70 105 125 200 0
stranded_cov25 = DelayedArray::DelayedArray(matrix(c(
40,100,1040,1500,0,
70,105,125,200,0
), ncol = 2))
#[-----------------------][-----------------------][-----------------------][-----------------------][]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# test1 methylation
# 4 0 9 0 35 900
# 4 5 19 0 1400
# test2 methylation
# 9 1 14 5 15 99
# 9 5 34 5 199
#[-----------------------][-----------------------][-----------------------][-----------------------][]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# tile_by_windows(bs = bsseq_stranded, win_size = 25) methylation
# 8 33 935 1400 0
# 19 58 119 199 0
stranded_meth25 = DelayedArray::DelayedArray(matrix(c(
8,33,935,1400,0,
19,58,119,199,0
), ncol = 2))
bsseq_stranded_win25 = BSseq(
gr = win25_stranded_gr,
Cov = stranded_cov25,
M = stranded_meth25,
pData = data.frame(row.names = c('test1','test2')),
sampleNames = c('test1','test2')
)
########################################
#[-----------------------][-----------------------][-----------------------][-----------------------]
#---------C--------------C--------------C---------C---------C--------------C-
# test1 coverage
# 10 100 30 0 40 2500
# test2 coverage
# 20 100 50 10 20 300
#[-----------------------][-----------------------][-----------------------][-----------------------]
#---------C--------------C--------------C---------C---------C--------------C-
# tile_by_windows(bs = bsseq_destranded, win_size = 25) coverage
# 110 30 2540 0
# 120 60 320 0
destranded_cov25 = DelayedArray::DelayedArray(matrix(c(
110,30,2540,0,
120,60,320,0
), ncol = 2))
#[-----------------------][-----------------------][-----------------------][-----------------------]
#---------C--------------C--------------C---------C---------C--------------C-
# test1 methylation
# 8 5 28 0 35 2300
# test2 methylation
# 18 6 48 10 15 298
#[-----------------------][-----------------------][-----------------------][-----------------------]
#---------C--------------C--------------C---------C---------C--------------C-
# tile_by_windows(bs = bsseq_destranded, win_size = 25) methylation
# 13 28 2335 0
# 24 58 313 0
destranded_meth25 = DelayedArray::DelayedArray(matrix(c(
13,28,2335,0,
24,58,313,0
), ncol = 2))
bsseq_destranded_win25 = BSseq(
gr = win25_destranded_gr,
Cov = destranded_cov25,
M = destranded_meth25,
pData = data.frame(row.names = c('test3','test4')),
sampleNames = c('test3','test4')
)
################################################################################
# win25_multichrom_gr
################################################################################
#[-----------------------][-----------------------][---]
#---------C---------C---------C
# test1 coverage / methylation
# 10 20 30
# test2 coverage / methylation
# 40 50 60
#[-----------------------][-----------------------][---]
#---------C---------C---------C
#[-----------------------][---]
#---------C
# test1 coverage / methylation
# 90
# test2 coverage / methylation
# 100
#[-----------------------][---]
#---------C
multichrom_cov25 = DelayedArray::DelayedArray(matrix(c(
30,30,0,90,0,
90,60,0,100,0
), ncol = 2))
multichrom_meth25 = multichrom_cov25
bsseq_multichrom_win25 = BSseq(
gr = win25_multichrom_gr,
Cov = multichrom_cov25,
M = multichrom_meth25,
pData = data.frame(row.names = c('test1','test2')),
sampleNames = c('test1','test2')
)
################################################################################
usethis::use_data(
gr_tiles1,
gr_tiles2,
gr_tiles3,
gr_tiles4,
gr_tiles5,
win25_stranded_gr,
win25_destranded_gr,
win25_multichrom_gr,
bsseq_stranded_tiled1,
bsseq_destranded_tiled1,
filter_loc_tiles1,
bsseq_stranded_tiled2,
bsseq_destranded_tiled2,
bsseq_stranded_tiled3,
bsseq_destranded_tiled3,
bsseq_stranded_tiled4,
bsseq_destranded_tiled4,
filter_loc_tiles4,
bsseq_stranded_tiled5,
bsseq_destranded_tiled5,
filter_loc_tiles5,
bsseq_stranded_win25,
bsseq_destranded_win25,
bsseq_multichrom_win25,
internal = TRUE,
overwrite = TRUE)
sartorlab/methylSig documentation built on Aug. 22, 2024, 5:58 p.m.
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library(bsseq)
library(DelayedArray)
library(GenomicRanges)
################################################################################
# Use for tile_by_regions() tests
# Use for filter_loci_by_location() tests
#----[---------]---------[--------------]----[---------]--------------[---------]
gr_tiles1 = GRanges(
seqnames = c('chr1','chr1','chr1','chr1'),
ranges = IRanges(
start = c(5,25,45,70),
end = c(15,40,55,80)
)
)
# Use for tiling tests
#----[------------------------]----[----------------------------------]----[----]
gr_tiles2 = GRanges(
seqnames = c('chr1','chr1','chr1'),
ranges = IRanges(
start = c(5,35,75),
end = c(30,70,80)
)
)
# Use for tiling tests
# Use for filter_loci_by_location() tests (expect an error from removing all)
#----[--------------------------------------------------------------------------]
gr_tiles3 = GRanges(
seqnames = c('chr1'),
ranges = IRanges(
start = c(5),
end = c(80)
)
)
# Use for tiling tests
# Use for filter_loci_by_location() tests
#----[--------------]------------------------------------------------------------
gr_tiles4 = GRanges(
seqnames = c('chr1'),
ranges = IRanges(
start = c(5),
end = c(20)
)
)
# Use for tiling tests
# Use for filter_loci_by_location() tests (expect nothing filtered)
#----[---]-----------------------------------------------------------------------
gr_tiles5 = GRanges(
seqnames = c('chr1'),
ranges = IRanges(
start = c(5),
end = c(9)
)
)
#[-----------------------][-----------------------][-----------------------][-----------------------][]
seqlengths = c('chr1' = 101)
win25_stranded_gr = GenomicRanges::tileGenome(
seqlengths = seqlengths,
tilewidth = 25,
cut.last.tile.in.chrom = TRUE)
#[-----------------------][-----------------------][-----------------------][-----------------------]
seqlengths = c('chr1' = 100)
win25_destranded_gr = GenomicRanges::tileGenome(
seqlengths = seqlengths,
tilewidth = 25,
cut.last.tile.in.chrom = TRUE)
#[-----------------------][-----------------------][---]
#[-----------------------][---]
seqlengths = c('chr1' = 55, 'chr2' = 35)
win25_multichrom_gr = GenomicRanges::tileGenome(
seqlengths = seqlengths,
tilewidth = 25,
cut.last.tile.in.chrom = TRUE)
################################################################################
# gr_tiles1
################################################################################
#----[---------]---------[--------------]----[---------]--------------[---------]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# test1 coverage
# 5 30 10 0 40 1000
# 5 70 20 0 1500
# test2 coverage
# 10 50 15 5 20 100
# 10 50 35 5 200
#----[---------]---------[--------------]----[---------]--------------[---------]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# tile_by_regions(bs = bsseq_stranded, gr = gr_tiles1) coverage
# 10 110 0 2500
# 20 115 10 300
stranded_cov1 = DelayedArray::DelayedArray(matrix(c(
10,110,0,2500,
20,115,10,300
), ncol = 2))
#----[---------]---------[--------------]----[---------]--------------[---------]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# test1 coverage
# 5 30 10 0 40 1000
# 5 70 20 0 1500
# test2 coverage
# 10 50 15 5 20 100
# 10 50 35 5 200
#----[---------]---------[--------------]----[---------]--------------[---------]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# filter_loci_by_location(bs = bsseq_stranded, gr = gr_tiles1) coverage
# 20 40
# 35 20
filter_cov1 = DelayedArray::DelayedArray(matrix(c(
20,40,
35,20
), ncol = 2))
#----[---------]---------[--------------]----[---------]--------------[---------]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# test1 methylation
# 4 0 9 0 35 900
# 4 5 19 0 1400
# test2 methylation
# 9 1 14 5 15 99
# 9 5 34 5 199
#----[---------]---------[--------------]----[---------]--------------[---------]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# tile_by_regions(bs = bsseq_stranded, gr = gr_tiles1) methylation
# 8 14 0 2300
# 18 20 10 298
stranded_meth1 = DelayedArray::DelayedArray(matrix(c(
8,14,0,2300,
18,20,10,298
), ncol = 2))
#----[---------]---------[--------------]----[---------]--------------[---------]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# test1 methylation
# 4 0 9 0 35 900
# 4 5 19 0 1400
# test2 methylation
# 9 1 14 5 15 99
# 9 5 34 5 199
#----[---------]---------[--------------]----[---------]--------------[---------]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# filter_loci_by_location(bs = bsseq_stranded, gr = gr_tiles1) methylation
# 19 35
# 34 15
filter_meth1 = DelayedArray::DelayedArray(matrix(c(
19,35,
34,15
), ncol = 2))
bsseq_stranded_tiled1 = BSseq(
gr = gr_tiles1,
Cov = stranded_cov1,
M = stranded_meth1,
pData = data.frame(row.names = c('test1','test2')),
sampleNames = c('test1','test2')
)
filter_loc_tiles1 = BSseq(
gr = granges(bsseq_stranded[c(6,9)]),
Cov = filter_cov1,
M = filter_meth1,
pData = data.frame(row.names = c('test1','test2')),
sampleNames = c('test1','test2')
)
########################################
#----[---------]---------[--------------]----[---------]--------------[---------]
#---------C--------------C--------------C---------C---------C--------------C-
# test1 coverage
# 10 100 30 0 40 2500
# test2 coverage
# 20 100 50 10 20 300
#----[---------]---------[--------------]----[---------]--------------[---------]
#---------C--------------C--------------C---------C---------C--------------C-
# tile_by_regions(bs = bsseq_destranded, gr = gr_tiles1) coverage
# 10 130 0 2500
# 20 150 10 300
destranded_cov1 = DelayedArray::DelayedArray(matrix(c(
10,130,0,2500,
20,150,10,300
), ncol = 2))
#----[---------]---------[--------------]----[---------]--------------[---------]
#---------C--------------C--------------C---------C---------C--------------C-
# test1 methylation
# 8 5 28 0 35 2300
# test2 methylation
# 18 6 48 10 15 298
#----[---------]---------[--------------]----[---------]--------------[---------]
#---------C--------------C--------------C---------C---------C--------------C-
# tile_by_regions(bs = bsseq_destranded, gr = gr_tiles1) methylation
# 8 14 0 2300
# 18 54 10 298
destranded_meth1 = DelayedArray::DelayedArray(matrix(c(
8,33,0,2300,
18,54,10,298
), ncol = 2))
bsseq_destranded_tiled1 = BSseq(
gr = gr_tiles1,
Cov = destranded_cov1,
M = destranded_meth1,
pData = data.frame(row.names = c('test3','test4')),
sampleNames = c('test3','test4')
)
################################################################################
# gr_tiles2
################################################################################
#----[------------------------]----[----------------------------------]----[----]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# test1 coverage
# 5 30 10 0 40 1000
# 5 70 20 0 1500
# test2 coverage
# 10 50 15 5 20 100
# 10 50 35 5 200
#----[------------------------]----[----------------------------------]----[----]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# tile_by_regions(bs = bsseq_stranded, gr = gr_tiles2) coverage
# 110 70 2500
# 120 80 300
stranded_cov2 = DelayedArray::DelayedArray(matrix(c(
110,70,2500,
120,80,300
), ncol = 2))
#----[------------------------]----[----------------------------------]----[----]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# test1 methylation
# 4 0 9 0 35 900
# 4 5 19 0 1400
# test2 methylation
# 9 1 14 5 15 99
# 9 5 34 5 199
#----[------------------------]----[----------------------------------]----[----]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# tile_by_regions(bs = bsseq_stranded, gr = gr_tiles2) methylation
# 13 63 2300
# 24 73 298
stranded_meth2 = DelayedArray::DelayedArray(matrix(c(
13,63,2300,
24,73,298
), ncol = 2))
bsseq_stranded_tiled2 = BSseq(
gr = gr_tiles2,
Cov = stranded_cov2,
M = stranded_meth2,
pData = data.frame(row.names = c('test1','test2')),
sampleNames = c('test1','test2')
)
########################################
#----[------------------------]----[----------------------------------]----[----]
#---------C--------------C--------------C---------C---------C--------------C-
# test1 coverage
# 10 100 30 0 40 2500
# test2 coverage
# 20 100 50 10 20 300
#----[------------------------]----[----------------------------------]----[----]
#---------C--------------C--------------C---------C---------C--------------C-
# tile_by_regions(bs = bsseq_destranded, gr = gr_tiles2) coverage
# 110 70 2500
# 120 80 300
destranded_cov2 = DelayedArray::DelayedArray(matrix(c(
110,70,2500,
120,80,300
), ncol = 2))
#----[------------------------]----[----------------------------------]----[----]
#---------C--------------C--------------C---------C---------C--------------C-
# test1 methylation
# 8 5 28 0 35 2300
# test2 methylation
# 18 6 48 10 15 298
#----[------------------------]----[----------------------------------]----[----]
#---------C--------------C--------------C---------C---------C--------------C-
# tile_by_regions(bs = bsseq_destranded, gr = gr_tiles2) methylation
# 13 63 2300
# 24 73 298
destranded_meth2 = DelayedArray::DelayedArray(matrix(c(
13,63,2300,
24,73,298
), ncol = 2))
bsseq_destranded_tiled2 = BSseq(
gr = gr_tiles2,
Cov = destranded_cov2,
M = destranded_meth2,
pData = data.frame(row.names = c('test3','test4')),
sampleNames = c('test3','test4')
)
################################################################################
# gr_tiles3
################################################################################
#----[--------------------------------------------------------------------------]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# test1 coverage
# 5 30 10 0 40 1000
# 5 70 20 0 1500
# test2 coverage
# 10 50 15 5 20 100
# 10 50 35 5 200
#----[--------------------------------------------------------------------------]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# tile_by_regions(bs = bsseq_stranded, gr = gr_tiles3) coverage
# 2680
# 500
stranded_cov3 = DelayedArray::DelayedArray(matrix(c(
2680,
500
), ncol = 2))
#----[--------------------------------------------------------------------------]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# test1 methylation
# 4 0 9 0 35 900
# 4 5 19 0 1400
# test2 methylation
# 9 1 14 5 15 99
# 9 5 34 5 199
#----[--------------------------------------------------------------------------]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# tile_by_regions(bs = bsseq_stranded, gr = gr_tiles3) methylation
# 2376
# 395
stranded_meth3 = DelayedArray::DelayedArray(matrix(c(
2376,
395
), ncol = 2))
bsseq_stranded_tiled3 = BSseq(
gr = gr_tiles3,
Cov = stranded_cov3,
M = stranded_meth3,
pData = data.frame(row.names = c('test1','test2')),
sampleNames = c('test1','test2')
)
########################################
#----[------------------------]----[----------------------------------]----[----]
#---------C--------------C--------------C---------C---------C--------------C-
# test1 coverage
# 10 100 30 0 40 2500
# test2 coverage
# 20 100 50 10 20 300
#----[------------------------]----[----------------------------------]----[----]
#---------C--------------C--------------C---------C---------C--------------C-
# tile_by_regions(bs = bsseq_destranded, gr = gr_tiles3) coverage
# 2680
# 500
destranded_cov3 = DelayedArray::DelayedArray(matrix(c(
2680,
500
), ncol = 2))
#----[------------------------]----[----------------------------------]----[----]
#---------C--------------C--------------C---------C---------C--------------C-
# test1 methylation
# 8 5 28 0 35 2300
# test2 methylation
# 18 6 48 10 15 298
#----[------------------------]----[----------------------------------]----[----]
#---------C--------------C--------------C---------C---------C--------------C-
# tile_by_regions(bs = bsseq_destranded, gr = gr_tiles3) methylation
# 2376
# 395
destranded_meth3 = DelayedArray::DelayedArray(matrix(c(
2376,
395
), ncol = 2))
bsseq_destranded_tiled3 = BSseq(
gr = gr_tiles3,
Cov = destranded_cov3,
M = destranded_meth3,
pData = data.frame(row.names = c('test3','test4')),
sampleNames = c('test3','test4')
)
################################################################################
# gr_tiles4
################################################################################
#----[--------------]------------------------------------------------------------
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# test1 coverage
# 5 30 10 0 40 1000
# 5 70 20 0 1500
# test2 coverage
# 10 50 15 5 20 100
# 10 50 35 5 200
#----[--------------]------------------------------------------------------------
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# tile_by_regions(bs = bsseq_stranded, gr = gr_tiles4) coverage
# 10
# 20
stranded_cov4 = DelayedArray::DelayedArray(matrix(c(
10,
20
), ncol = 2))
filter_cov4 = DelayedArray::DelayedArray(matrix(c(
30,70,10,20,0,0,40,1000,1500,
50,50,15,35,5,5,20,100,200
), ncol = 2))
#----[--------------]------------------------------------------------------------
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# test1 methylation
# 4 0 9 0 35 900
# 4 5 19 0 1400
# test2 methylation
# 9 1 14 5 15 99
# 9 5 34 5 199
#----[--------------]------------------------------------------------------------
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# tile_by_regions(bs = bsseq_stranded, gr = gr_tiles4) methylation
# 8
# 18
stranded_meth4 = DelayedArray::DelayedArray(matrix(c(
8,
18
), ncol = 2))
filter_meth4 = DelayedArray::DelayedArray(matrix(c(
0,5,9,19,0,0,35,900,1400,
1,5,14,34,5,5,15,99,199
), ncol = 2))
bsseq_stranded_tiled4 = BSseq(
gr = gr_tiles4,
Cov = stranded_cov4,
M = stranded_meth4,
pData = data.frame(row.names = c('test1','test2')),
sampleNames = c('test1','test2')
)
filter_loc_tiles4 = BSseq(
gr = granges(bsseq_stranded[-c(1,2)]),
Cov = filter_cov4,
M = filter_meth4,
pData = data.frame(row.names = c('test1','test2')),
sampleNames = c('test1','test2')
)
########################################
#----[--------------]------------------------------------------------------------
#---------C--------------C--------------C---------C---------C--------------C-
# test1 coverage
# 10 100 30 0 40 2500
# test2 coverage
# 20 100 50 10 20 300
#----[--------------]------------------------------------------------------------
#---------C--------------C--------------C---------C---------C--------------C-
# tile_by_regions(bs = bsseq_destranded, gr = gr_tiles4) coverage
# 10
# 20
destranded_cov4 = DelayedArray::DelayedArray(matrix(c(
10,
20
), ncol = 2))
#----[--------------]------------------------------------------------------------
#---------C--------------C--------------C---------C---------C--------------C-
# test1 methylation
# 8 5 28 0 35 2300
# test2 methylation
# 18 6 48 10 15 298
#----[--------------]------------------------------------------------------------
#---------C--------------C--------------C---------C---------C--------------C-
# tile_by_regions(bs = bsseq_destranded, gr = gr_tiles4) methylation
# 8
# 18
destranded_meth4 = DelayedArray::DelayedArray(matrix(c(
8,
18
), ncol = 2))
bsseq_destranded_tiled4 = BSseq(
gr = gr_tiles4,
Cov = destranded_cov4,
M = destranded_meth4,
pData = data.frame(row.names = c('test3','test4')),
sampleNames = c('test3','test4')
)
################################################################################
# gr_tiles5
################################################################################
#----[---]-----------------------------------------------------------------------
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# test1 coverage
# 5 30 10 0 40 1000
# 5 70 20 0 1500
# test2 coverage
# 10 50 15 5 20 100
# 10 50 35 5 200
#----[---]-----------------------------------------------------------------------
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# tile_by_regions(bs = bsseq_stranded, gr = gr_tiles5) coverage
# 0
# 0
stranded_cov5 = DelayedArray::DelayedArray(matrix(c(
0,
0
), ncol = 2))
#----[---]-----------------------------------------------------------------------
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# test1 methylation
# 4 0 9 0 35 900
# 4 5 19 0 1400
# test2 methylation
# 9 1 14 5 15 99
# 9 5 34 5 199
#----[---]-----------------------------------------------------------------------
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# tile_by_regions(bs = bsseq_stranded, gr = gr_tiles5) methylation
# 0
# 0
stranded_meth5 = DelayedArray::DelayedArray(matrix(c(
0,
0
), ncol = 2))
bsseq_stranded_tiled5 = BSseq(
gr = gr_tiles5,
Cov = stranded_cov5,
M = stranded_meth5,
pData = data.frame(row.names = c('test1','test2')),
sampleNames = c('test1','test2')
)
########################################
#----[---]-----------------------------------------------------------------------
#---------C--------------C--------------C---------C---------C--------------C-
# test1 coverage
# 10 100 30 0 40 2500
# test2 coverage
# 20 100 50 10 20 300
#----[---]-----------------------------------------------------------------------
#---------C--------------C--------------C---------C---------C--------------C-
# tile_by_regions(bs = bsseq_destranded, gr = gr_tiles5) coverage
# 0
# 0
destranded_cov5 = DelayedArray::DelayedArray(matrix(c(
0,
0
), ncol = 2))
#----[---]-----------------------------------------------------------------------
#---------C--------------C--------------C---------C---------C--------------C-
# test1 methylation
# 8 5 28 0 35 2300
# test2 methylation
# 18 6 48 10 15 298
#----[---]-----------------------------------------------------------------------
#---------C--------------C--------------C---------C---------C--------------C-
# tile_by_regions(bs = bsseq_destranded, gr = gr_tiles5) methylation
# 0
# 0
destranded_meth5 = DelayedArray::DelayedArray(matrix(c(
0,
0
), ncol = 2))
bsseq_destranded_tiled5 = BSseq(
gr = gr_tiles5,
Cov = destranded_cov5,
M = destranded_meth5,
pData = data.frame(row.names = c('test3','test4')),
sampleNames = c('test3','test4')
)
filter_loc_tiles5 = bsseq_stranded
################################################################################
# win25_gr
################################################################################
#[-----------------------][-----------------------][-----------------------][-----------------------][]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# test1 coverage
# 5 30 10 0 40 1000
# 5 70 20 0 1500
# test2 coverage
# 10 50 15 5 20 100
# 10 50 35 5 200
#[-----------------------][-----------------------][-----------------------][-----------------------][]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# tile_by_windows(bs = bsseq_stranded, win_size = 25) coverage
# 40 100 1040 1500 0
# 70 105 125 200 0
stranded_cov25 = DelayedArray::DelayedArray(matrix(c(
40,100,1040,1500,0,
70,105,125,200,0
), ncol = 2))
#[-----------------------][-----------------------][-----------------------][-----------------------][]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# test1 methylation
# 4 0 9 0 35 900
# 4 5 19 0 1400
# test2 methylation
# 9 1 14 5 15 99
# 9 5 34 5 199
#[-----------------------][-----------------------][-----------------------][-----------------------][]
#---------CG-------------CG-------------CG--------CG--------C--------------CG
# tile_by_windows(bs = bsseq_stranded, win_size = 25) methylation
# 8 33 935 1400 0
# 19 58 119 199 0
stranded_meth25 = DelayedArray::DelayedArray(matrix(c(
8,33,935,1400,0,
19,58,119,199,0
), ncol = 2))
bsseq_stranded_win25 = BSseq(
gr = win25_stranded_gr,
Cov = stranded_cov25,
M = stranded_meth25,
pData = data.frame(row.names = c('test1','test2')),
sampleNames = c('test1','test2')
)
########################################
#[-----------------------][-----------------------][-----------------------][-----------------------]
#---------C--------------C--------------C---------C---------C--------------C-
# test1 coverage
# 10 100 30 0 40 2500
# test2 coverage
# 20 100 50 10 20 300
#[-----------------------][-----------------------][-----------------------][-----------------------]
#---------C--------------C--------------C---------C---------C--------------C-
# tile_by_windows(bs = bsseq_destranded, win_size = 25) coverage
# 110 30 2540 0
# 120 60 320 0
destranded_cov25 = DelayedArray::DelayedArray(matrix(c(
110,30,2540,0,
120,60,320,0
), ncol = 2))
#[-----------------------][-----------------------][-----------------------][-----------------------]
#---------C--------------C--------------C---------C---------C--------------C-
# test1 methylation
# 8 5 28 0 35 2300
# test2 methylation
# 18 6 48 10 15 298
#[-----------------------][-----------------------][-----------------------][-----------------------]
#---------C--------------C--------------C---------C---------C--------------C-
# tile_by_windows(bs = bsseq_destranded, win_size = 25) methylation
# 13 28 2335 0
# 24 58 313 0
destranded_meth25 = DelayedArray::DelayedArray(matrix(c(
13,28,2335,0,
24,58,313,0
), ncol = 2))
bsseq_destranded_win25 = BSseq(
gr = win25_destranded_gr,
Cov = destranded_cov25,
M = destranded_meth25,
pData = data.frame(row.names = c('test3','test4')),
sampleNames = c('test3','test4')
)
################################################################################
# win25_multichrom_gr
################################################################################
#[-----------------------][-----------------------][---]
#---------C---------C---------C
# test1 coverage / methylation
# 10 20 30
# test2 coverage / methylation
# 40 50 60
#[-----------------------][-----------------------][---]
#---------C---------C---------C
#[-----------------------][---]
#---------C
# test1 coverage / methylation
# 90
# test2 coverage / methylation
# 100
#[-----------------------][---]
#---------C
multichrom_cov25 = DelayedArray::DelayedArray(matrix(c(
30,30,0,90,0,
90,60,0,100,0
), ncol = 2))
multichrom_meth25 = multichrom_cov25
bsseq_multichrom_win25 = BSseq(
gr = win25_multichrom_gr,
Cov = multichrom_cov25,
M = multichrom_meth25,
pData = data.frame(row.names = c('test1','test2')),
sampleNames = c('test1','test2')
)
################################################################################
usethis::use_data(
gr_tiles1,
gr_tiles2,
gr_tiles3,
gr_tiles4,
gr_tiles5,
win25_stranded_gr,
win25_destranded_gr,
win25_multichrom_gr,
bsseq_stranded_tiled1,
bsseq_destranded_tiled1,
filter_loc_tiles1,
bsseq_stranded_tiled2,
bsseq_destranded_tiled2,
bsseq_stranded_tiled3,
bsseq_destranded_tiled3,
bsseq_stranded_tiled4,
bsseq_destranded_tiled4,
filter_loc_tiles4,
bsseq_stranded_tiled5,
bsseq_destranded_tiled5,
filter_loc_tiles5,
bsseq_stranded_win25,
bsseq_destranded_win25,
bsseq_multichrom_win25,
internal = TRUE,
overwrite = TRUE)
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