Nothing
## ----setup, include=FALSE, cache=FALSE----------------------------------------
library(knitr)
# set global chunk options
opts_chunk$set(concordance=TRUE)
## ----options,echo=FALSE-----------------------------------
options(width=60)
## ----Genomic Features-------------------------------------
library(Guitar)
# genomic features imported into named list
stBedFiles <- list(system.file("extdata", "m6A_mm10_exomePeak_1000peaks_bed12.bed",
package="Guitar"))
## ----label=quick_plot,eval=FALSE--------------------------
# count <- GuitarPlot(txGenomeVer = "mm10",
# stBedFiles = stBedFiles,
# miscOutFilePrefix = NA)
#
## ----Guitar coordiantes-----------------------------------
txdb_file <- system.file("extdata", "mm10_toy.sqlite",
package="Guitar")
txdb <- loadDb(txdb_file)
guitarTxdb <- makeGuitarTxdb(txdb = txdb, txPrimaryOnly = FALSE)
# Or use gff. file to generate guitarTxdb
# Or use getTxdb() to download TxDb from internet:
# txdb <- getTxdb(txGenomeVer="hg19")
# guitarTxdb <- makeGuitarTxdb(txdb)
## ----label=example,echo=TRUE,fig.height=6,fig.width=12----
GuitarPlot(txTxdb = txdb,
stBedFiles = stBedFiles,
miscOutFilePrefix = "example")
## ----label=parameter_1,echo=TRUE,fig.height=6,fig.width=12----
GuitarPlot(txTxdb = txdb,
stBedFiles = stBedFiles,
headOrtail = TRUE)
## ----label=parameter_2,echo=TRUE,fig.height=6,fig.width=12----
GuitarPlot(txTxdb = txdb,
stBedFiles = stBedFiles,
headOrtail = TRUE,
enableCI = FALSE)
## ----label=mm10_example,echo=TRUE,fig.height=6,fig.width=12----
# import different data formats into a named list object.
# These genomic features are using mm10 genome assembly
stBedFiles <- list(system.file("extdata", "m6A_mm10_exomePeak_1000peaks_bed12.bed",
package="Guitar"),
system.file("extdata", "m6A_mm10_exomePeak_1000peaks_bed6.bed",
package="Guitar"))
# Build Guitar Coordinates
txdb_file <- system.file("extdata", "mm10_toy.sqlite",
package="Guitar")
txdb <- loadDb(txdb_file)
# Guitar Plot
GuitarPlot(txTxdb = txdb,
stBedFiles = stBedFiles,
headOrtail = TRUE,
enableCI = FALSE,
mapFilterTranscript = TRUE,
pltTxType = c("mrna"),
stGroupName = c("BED12","BED6"))
## ----label=sample,echo=TRUE,fig.height=6,fig.width=12-----
stGRangeLists = vector("list", length(stBedFiles))
sitesPoints <- list()
for (i in seq_len(length(stBedFiles))) {
stGRangeLists[[i]] <- blocks(import(stBedFiles[[i]]))
}
for (i in seq_len(length(stGRangeLists))) {
sitesPoints[[i]] <- samplePoints(stGRangeLists[i],
stSampleNum = 10,
stAmblguity = 5,
pltTxType = c("mrna"),
stSampleModle = "Equidistance",
mapFilterTranscript = FALSE,
guitarTxdb = guitarTxdb)
}
## ----label=GuitarTxdb,eval=TRUE---------------------------
guitarTxdb <- makeGuitarTxdb(txdb = txdb,
txAmblguity = 5,
txMrnaComponentProp = c(0.1,0.15,0.6,0.05,0.1),
txLncrnaComponentProp = c(0.2,0.6,0.2),
pltTxType = c("tx","mrna","ncrna"),
txPrimaryOnly = FALSE)
## ----label=Check,echo=TRUE,fig.height=6,fig.width=12------
gcl <- list(guitarTxdb$tx$tx)
GuitarPlot(txTxdb = txdb,
stGRangeLists = gcl,
stSampleNum = 200,
enableCI = TRUE,
pltTxType = c("tx"),
txPrimaryOnly = FALSE
)
## ----label=tx_comp,eval=TRUE------------------------------
GuitarCoords <- guitarTxdb$tx$txComponentGRange
type <- paste(mcols(GuitarCoords)$componentType,mcols(GuitarCoords)$txType)
key <- unique(type)
landmark <- list(1,2,3,4,5,6,7,8,9,10,11)
names(landmark) <- key
for (i in 1:length(key)) {
landmark[[i]] <- GuitarCoords[type==key[i]]
}
GuitarPlot(txTxdb = txdb ,
stGRangeLists = landmark[1:3],
pltTxType = c("tx"),
enableCI = FALSE
)
## ----label=mrna_comp,eval=TRUE----------------------------
GuitarPlot(txTxdb = txdb ,
stGRangeLists = landmark[4:8],
pltTxType = c("mrna"),
enableCI = FALSE
)
## ----label=comp,eval=TRUE---------------------------------
GuitarPlot(txTxdb = txdb ,
stGRangeLists = landmark[9:11],
pltTxType = c("ncrna"),
enableCI = FALSE
)
## ----label=session,eval=TRUE------------------------------
sessionInfo()
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