tests/testthat/testVastToolsEvents.R
In nuno-agostinho/psichomics: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
context("Parse VAST-TOOLS splicing events")
test_that("parseVastToolsAnnotation parses annotation from VAST-tools", {
folder <- "extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES"
vastToolsOutput <- system.file(folder, package="psichomics")
vast <- parseVastToolsAnnotation(vastToolsOutput)
expect_is(vast, "ASevents")
expect_equal(length(vast), 14)
expect_equal(unique(vast$Program), "VAST-TOOLS")
expect_equal(unique(vast$Strand), c("-", "+"))
})
test_that("parseVastToolsEvent parses exon skipping event", {
events <- read.table(
text = "
NFYA HsaEX0042823 chr6:41046768-41046903 136 chr6:41040823,41046768-41046903,41051785 C2 0 N,N,N,Bn,S@0,0 0 N,N,N,Bn,S@0,0
SCYL3 HsaEX0056691 chr1:169839396-169839498 103 chr1:169842837,169839396-169839498,169838180+169838269 S 0.00 N,N,N,Bn,S@0,0 0.00 N,N,N,Bn,S@0,0
LAP3 HsaEX0035325 chr4:17587574-17587861 288 chr4:17586759,17587574-17587861,17590442 S 0.00 N,N,N,Bn,S@0,0 0.00 N,N,N,Bn,S@0,0
")
parsed <- parseVastToolsEvent(events)
expect_is(parsed, "data.frame")
expect_equal(nrow(parsed), 3)
expect_equal(parsed$Program[[1]], "VAST-TOOLS")
expect_equal(parsed$Gene.symbol[[1]], "NFYA")
expect_equal(parsed$Inclusion.level.A[[1]], 0)
expect_equal(parsed$Inclusion.level.B[[1]], 0)
expect_equal(parsed$C1.end[[1]], 41040823)
expect_equal(parsed$Event.type[[1]], "SE")
expect_equal(parsed$Strand[[1]], "+")
expect_equal(parsed$Program[[2]], "VAST-TOOLS")
expect_equal(parsed$Gene.symbol[[2]], "SCYL3")
expect_equal(parsed$Inclusion.level.A[[2]], 0)
expect_equal(parsed$Inclusion.level.B[[2]], 0)
expect_equal(parsed$C1.end[[2]], 169842837)
expect_equal(parsed$Event.type[[2]], "SE")
expect_equal(parsed$Strand[[2]], "-")
expect_equal(parsed$Program[[3]], "VAST-TOOLS")
expect_equal(parsed$Gene.symbol[[3]], "LAP3")
expect_equal(parsed$Inclusion.level.A[[3]], 0)
expect_equal(parsed$Inclusion.level.B[[3]], 0)
expect_equal(parsed$C1.end[[3]], 17586759)
expect_equal(parsed$Event.type[[3]], "SE")
expect_equal(parsed$Strand[[3]], "+")
})
test_that("parseVastToolsEvent parses exon skipping annotation", {
event <- read.table(
text = "
NFYA HsaEX0042823 chr6:41046768-41046903 136 chr6:41040823,41046768-41046903,41051785 C2
")
parsed <- parseVastToolsEvent(event)
expect_equal(parsed$Program[[1]], "VAST-TOOLS")
expect_equal(parsed$Gene.symbol[[1]], "NFYA")
expect_equal(parsed$Event.ID[[1]], "HsaEX0042823")
expect_equal(parsed$Event.type[[1]], "SE")
expect_null(parsed$Inclusion.level.A)
expect_null(parsed$Inclusion.level.B)
expect_equal(parsed$Chromosome[[1]], "chr6")
expect_equal(parsed$Strand[[1]], "+")
expect_equal(parsed$C1.end[[1]], 41040823)
expect_equal(parsed$A1.start[[1]], 41046768)
expect_equal(parsed$A1.end[[1]], 41046903)
expect_equal(parsed$C2.start[[1]], 41051785)
})
test_that("parseVastToolsEvent parses alt. 3' splice site annotation", {
events <- read.table(
text = "
DPM1 ENSG00000000419-8-11,8-10-1/2 chr20:49557402-49557470 0 chr20:49558568,49557402-49557492+49557470 Alt3
DPM1 ENSG00000000419-8-11,8-10-2/2 chr20:49557402-49557492 22 chr20:49558568,49557402-49557492+49557470 Alt3
C1orf112 ENSG00000000460-14-19,14-18-1/2 chr1:169773253-169773381 0 chr1:169772450,169773253+169773216-169773381 Alt3
")
parsed <- parseVastToolsEvent(events)
expect_is(parsed, "data.frame")
expect_equal(nrow(parsed), 3)
expect_equal(parsed$Program[[1]], "VAST-TOOLS")
expect_equal(parsed$C1.end[[1]], 49558568)
expect_equal(parsed$A1.start[[1]], 49557492)
expect_equal(parsed$A2.start[[1]], 49557470)
expect_equal(parsed$A2.end[[1]], 49557402)
expect_equal(parsed$Event.type[[1]], "A3SS")
expect_equal(parsed$Strand[[1]], "-")
expect_equal(parsed$C1.end[[2]], 49558568)
expect_equal(parsed$A1.start[[2]], 49557492)
expect_equal(parsed$A2.start[[2]], 49557470)
expect_equal(parsed$A2.end[[2]], 49557402)
expect_equal(parsed$Event.type[[2]], "A3SS")
expect_equal(parsed$Strand[[2]], "-")
expect_equal(parsed$C1.end[[3]], 169772450)
expect_equal(parsed$A1.start[[3]], 169773253)
expect_equal(parsed$A2.start[[3]], 169773216)
expect_equal(parsed$A2.end[[3]], 169773381)
expect_equal(parsed$Event.type[[3]], "A3SS")
expect_equal(parsed$Strand[[3]], "+")
})
test_that("parseVastToolsEvent parses alt. 3' splice site annotation with information missing", {
events <- read.table(
text = "DPM1 ENSG00000000419-8-11,8-10-1/2 chr20:49557402-49557470 0 chr20:49558568,-49557492+49557470 Alt3
DPM1 ENSG00000000419-8-11,8-10-2/2 chr20:49557402-49557492 22 chr20:49558568,-49557492+49557470 Alt3
C1orf112 ENSG00000000460-14-19,14-18-1/2 chr1:169773253-169773381 0 chr1:169772450,169773253+169773216- Alt3")
parsed <- parseVastToolsEvent(events)
expect_is(parsed, "data.frame")
expect_equal(nrow(parsed), 3)
expect_equal(parsed$Program[[1]], "VAST-TOOLS")
expect_equal(parsed$C1.end[[1]], 49558568)
expect_equal(parsed$A1.start[[1]], 49557492)
expect_equal(parsed$A2.start[[1]], 49557470)
expect_true(is.na(parsed$A2.end[[1]]))
expect_equal(parsed$Event.type[[1]], "A3SS")
expect_equal(parsed$Strand[[1]], "-")
expect_equal(parsed$C1.end[[2]], 49558568)
expect_equal(parsed$A1.start[[2]], 49557492)
expect_equal(parsed$A2.start[[2]], 49557470)
expect_true(is.na(parsed$A2.end[[2]]))
expect_equal(parsed$Event.type[[2]], "A3SS")
expect_equal(parsed$Strand[[2]], "-")
expect_equal(parsed$C1.end[[3]], 169772450)
expect_equal(parsed$A1.start[[3]], 169773253)
expect_equal(parsed$A2.start[[3]], 169773216)
expect_true(is.na(parsed$A2.end[[3]]))
expect_equal(parsed$Event.type[[3]], "A3SS")
expect_equal(parsed$Strand[[3]], "+")
})
test_that("parseVastToolsEvent parses alt. 5' splice site annotation", {
events <- read.table(
text = "
TSPAN6 ENSG00000000003-2-4,3-4-1/2 chrX:99891605-99891686 0 chrX:99891605+99891188-99891686,99890743 Alt5
DPM1 ENSG00000000419-9-11,10-11-1/2 chr20:49557666-49557746 0 chr20:49557666+49557642-49557746,49557470 Alt5
NFYA ENSG00000001167-3-4,4-4-1/2 chr6:41048553-41048633 0 chr6:41048553-41048633+41048636,41051785 Alt5
")
parsed <- parseVastToolsEvent(events)
expect_is(parsed, "data.frame")
expect_equal(nrow(parsed), 3)
expect_equal(parsed$Program[[1]], "VAST-TOOLS")
expect_equal(parsed$A2.start[[1]], 99891686)
expect_equal(parsed$A2.end[[1]], 99891188)
expect_equal(parsed$A1.end[[1]], 99891605)
expect_equal(parsed$C2.start[[1]], 99890743)
expect_equal(parsed$Event.type[[1]], "A5SS")
expect_equal(parsed$Strand[[1]], "-")
expect_equal(parsed$A2.start[[2]], 49557746)
expect_equal(parsed$A2.end[[2]], 49557642)
expect_equal(parsed$A1.end[[2]], 49557666)
expect_equal(parsed$C2.start[[2]], 49557470)
expect_equal(parsed$Event.type[[2]], "A5SS")
expect_equal(parsed$Strand[[2]], "-")
expect_equal(parsed$A2.start[[3]], 41048553)
expect_equal(parsed$A2.end[[3]], 41048636)
expect_equal(parsed$A1.end[[3]], 41048633)
expect_equal(parsed$C2.start[[3]], 41051785)
expect_equal(parsed$Event.type[[3]], "A5SS")
expect_equal(parsed$Strand[[3]], "+")
})
test_that("parseVastToolsEvent parses alt. 5' splice site annotation with information missing", {
events <- read.table(
text = "
TSPAN6 ENSG00000000003-2-4,3-4-1/2 chrX:99891605-99891686 0 chrX:99891605+99891188-,99890743 Alt5
DPM1 ENSG00000000419-9-11,10-11-1/2 chr20:49557666-49557746 0 chr20:49557666+49557642-,49557470 Alt5
NFYA ENSG00000001167-3-4,4-4-1/2 chr6:41048553-41048633 0 chr6:-41048633+41048636,41051785 Alt5
")
parsed <- parseVastToolsEvent(events)
expect_is(parsed, "data.frame")
expect_equal(nrow(parsed), 3)
expect_equal(parsed$Program[[1]], "VAST-TOOLS")
expect_true(is.na(parsed$A2.start[[1]]))
expect_equal(parsed$A2.end[[1]], 99891188)
expect_equal(parsed$A1.end[[1]], 99891605)
expect_equal(parsed$C2.start[[1]], 99890743)
expect_equal(parsed$Event.type[[1]], "A5SS")
expect_equal(parsed$Strand[[1]], "-")
expect_true(is.na(parsed$A2.start[[2]]))
expect_equal(parsed$A2.end[[2]], 49557642)
expect_equal(parsed$A1.end[[2]], 49557666)
expect_equal(parsed$C2.start[[2]], 49557470)
expect_equal(parsed$Event.type[[2]], "A5SS")
expect_equal(parsed$Strand[[2]], "-")
expect_true(is.na(parsed$A2.start[[3]]))
expect_equal(parsed$A2.end[[3]], 41048636)
expect_equal(parsed$A1.end[[3]], 41048633)
expect_equal(parsed$C2.start[[3]], 41051785)
expect_equal(parsed$Event.type[[3]], "A5SS")
expect_equal(parsed$Strand[[3]], "+")
})
test_that("parseVastToolsEvent parses retained intron annotation", {
events <- read.table(
text = "
A2M ENSG00000175899-A2M:NM_000014:9 chr12:9258942-9259086 145 chr12:9259087-9259201=9258832-9258941:- IR-S A2M:NM_000014:9
A2ML1 ENSG00000166535-A2ML1:NM_144670:1 chr12:8975310-8975777 468 chr12:8975150-8975309=8975778-8975961:+ IR-S A2ML1:NM_144670:1
A2ML1 ENSG00000166535-A2ML1:NM_144670:10 chr12:8991819-8993964 2146 chr12:8991709-8991818=8993965-8994132:+ IR-S A2ML1:NM_144670:10
")
parsed <- parseVastToolsEvent(events)
expect_is(parsed, "data.frame")
expect_equal(nrow(parsed), 3)
expect_equal(parsed$Program[[1]], "VAST-TOOLS")
expect_equal(parsed$C1.start[[1]], 9259201)
expect_equal(parsed$C1.end[[1]], 9259087)
expect_equal(parsed$C2.start[[1]], 9258941)
expect_equal(parsed$C2.end[[1]], 9258832)
expect_equal(parsed$Event.type[[1]], "RI")
expect_equal(parsed$Strand[[1]], "-")
expect_equal(parsed$C1.start[[2]], 8975150)
expect_equal(parsed$C1.end[[2]], 8975309)
expect_equal(parsed$C2.start[[2]], 8975778)
expect_equal(parsed$C2.end[[2]], 8975961)
expect_equal(parsed$Event.type[[2]], "RI")
expect_equal(parsed$Strand[[2]], "+")
expect_equal(parsed$C1.start[[3]], 8991709)
expect_equal(parsed$C1.end[[3]], 8991818)
expect_equal(parsed$C2.start[[3]], 8993965)
expect_equal(parsed$C2.end[[3]], 8994132)
expect_equal(parsed$Event.type[[3]], "RI")
expect_equal(parsed$Strand[[3]], "+")
})
test_that("parseVastToolsSE parses exon skipping junctions", {
junctions <- read.table(
text = "
169768099 169770024 169770112 169771762
99887482 99885756 99885863 99884983
")
parsed <- parseVastToolsSE(junctions)
expect_equal(parsed$Strand[[1]], "+")
expect_equal(parsed$C1.end[[1]], 169768099)
expect_equal(parsed$A1.start[[1]], 169770024)
expect_equal(parsed$A1.end[[1]], 169770112)
expect_equal(parsed$C2.start[[1]], 169771762)
expect_equal(parsed$Strand[[2]], "-")
expect_equal(parsed$C1.end[[2]], 99887482)
expect_equal(parsed$A1.start[[2]], 99885863)
expect_equal(parsed$A1.end[[2]], 99885756)
expect_equal(parsed$C2.start[[2]], 99884983)
})
test_that("parseVastToolsRI parses retained intron junctions", {
junctions <- read.table(
text = "
125549925 125550263 125558422 125558525
58864658 58864693 58864294 58864563
")
parsed <- parseVastToolsRI(junctions, c("+", "-"))
expect_equal(parsed$Strand[[1]], "+")
expect_equal(parsed$C1.start[[1]], 125549925)
expect_equal(parsed$C1.end[[1]], 125550263)
expect_equal(parsed$C2.start[[1]], 125558422)
expect_equal(parsed$C2.end[[1]], 125558525)
expect_equal(parsed$Strand[[2]], "-")
expect_equal(parsed$C1.start[[2]], 58864693)
expect_equal(parsed$C1.end[[2]], 58864658)
expect_equal(parsed$C2.start[[2]], 58864563)
expect_equal(parsed$C2.end[[2]], 58864294)
})
test_that("parseVastToolsA3SS parses alt. 3' splice site junctions", {
junctions <- rbind(
c(36276385, list(c(36277798, 36277315)), 36277974),
c(7133604, 7133377, list(c(7133474, 7133456)))
)
parsed <- parseVastToolsA3SS(junctions)
expect_equal(parsed$Strand[[1]], "+")
expect_equal(parsed$C1.end[[1]], 36276385)
expect_equal(parsed$A1.start[[1]], 36277798)
expect_equal(parsed$A2.start[[1]], 36277315)
expect_equal(parsed$A2.end[[1]], 36277974)
expect_equal(parsed$Strand[[2]], "-")
expect_equal(parsed$C1.end[[2]], 7133604)
expect_equal(parsed$A1.start[[2]], 7133474)
expect_equal(parsed$A2.start[[2]], 7133456)
expect_equal(parsed$A2.end[[2]], 7133377)
})
test_that("parseVastToolsA5SS parses alt. 5' splice site junctions", {
junctions <- rbind(
c(74650610, list(c(74650654, 74650658)), 74650982),
c(list(c(49557666, 49557642), 49557746, 49557470))
)
parsed <- parseVastToolsA5SS(junctions)
expect_equal(parsed$Strand, c("+", "-"))
# Plus strand
expect_equal(parsed$A2.start[[1]], 74650610)
expect_equal(parsed$A2.end[[1]], 74650658)
expect_equal(parsed$A1.end[[1]], 74650654)
expect_equal(parsed$C2.start[[1]], 74650982)
# Minus strand
expect_equal(parsed$A2.start[[2]], 49557746)
expect_equal(parsed$A2.end[[2]], 49557642)
expect_equal(parsed$A1.end[[2]], 49557666)
expect_equal(parsed$C2.start[[2]], 49557470)
})
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context("Parse VAST-TOOLS splicing events")
test_that("parseVastToolsAnnotation parses annotation from VAST-tools", {
folder <- "extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES"
vastToolsOutput <- system.file(folder, package="psichomics")
vast <- parseVastToolsAnnotation(vastToolsOutput)
expect_is(vast, "ASevents")
expect_equal(length(vast), 14)
expect_equal(unique(vast$Program), "VAST-TOOLS")
expect_equal(unique(vast$Strand), c("-", "+"))
})
test_that("parseVastToolsEvent parses exon skipping event", {
events <- read.table(
text = "
NFYA HsaEX0042823 chr6:41046768-41046903 136 chr6:41040823,41046768-41046903,41051785 C2 0 N,N,N,Bn,S@0,0 0 N,N,N,Bn,S@0,0
SCYL3 HsaEX0056691 chr1:169839396-169839498 103 chr1:169842837,169839396-169839498,169838180+169838269 S 0.00 N,N,N,Bn,S@0,0 0.00 N,N,N,Bn,S@0,0
LAP3 HsaEX0035325 chr4:17587574-17587861 288 chr4:17586759,17587574-17587861,17590442 S 0.00 N,N,N,Bn,S@0,0 0.00 N,N,N,Bn,S@0,0
")
parsed <- parseVastToolsEvent(events)
expect_is(parsed, "data.frame")
expect_equal(nrow(parsed), 3)
expect_equal(parsed$Program[[1]], "VAST-TOOLS")
expect_equal(parsed$Gene.symbol[[1]], "NFYA")
expect_equal(parsed$Inclusion.level.A[[1]], 0)
expect_equal(parsed$Inclusion.level.B[[1]], 0)
expect_equal(parsed$C1.end[[1]], 41040823)
expect_equal(parsed$Event.type[[1]], "SE")
expect_equal(parsed$Strand[[1]], "+")
expect_equal(parsed$Program[[2]], "VAST-TOOLS")
expect_equal(parsed$Gene.symbol[[2]], "SCYL3")
expect_equal(parsed$Inclusion.level.A[[2]], 0)
expect_equal(parsed$Inclusion.level.B[[2]], 0)
expect_equal(parsed$C1.end[[2]], 169842837)
expect_equal(parsed$Event.type[[2]], "SE")
expect_equal(parsed$Strand[[2]], "-")
expect_equal(parsed$Program[[3]], "VAST-TOOLS")
expect_equal(parsed$Gene.symbol[[3]], "LAP3")
expect_equal(parsed$Inclusion.level.A[[3]], 0)
expect_equal(parsed$Inclusion.level.B[[3]], 0)
expect_equal(parsed$C1.end[[3]], 17586759)
expect_equal(parsed$Event.type[[3]], "SE")
expect_equal(parsed$Strand[[3]], "+")
})
test_that("parseVastToolsEvent parses exon skipping annotation", {
event <- read.table(
text = "
NFYA HsaEX0042823 chr6:41046768-41046903 136 chr6:41040823,41046768-41046903,41051785 C2
")
parsed <- parseVastToolsEvent(event)
expect_equal(parsed$Program[[1]], "VAST-TOOLS")
expect_equal(parsed$Gene.symbol[[1]], "NFYA")
expect_equal(parsed$Event.ID[[1]], "HsaEX0042823")
expect_equal(parsed$Event.type[[1]], "SE")
expect_null(parsed$Inclusion.level.A)
expect_null(parsed$Inclusion.level.B)
expect_equal(parsed$Chromosome[[1]], "chr6")
expect_equal(parsed$Strand[[1]], "+")
expect_equal(parsed$C1.end[[1]], 41040823)
expect_equal(parsed$A1.start[[1]], 41046768)
expect_equal(parsed$A1.end[[1]], 41046903)
expect_equal(parsed$C2.start[[1]], 41051785)
})
test_that("parseVastToolsEvent parses alt. 3' splice site annotation", {
events <- read.table(
text = "
DPM1 ENSG00000000419-8-11,8-10-1/2 chr20:49557402-49557470 0 chr20:49558568,49557402-49557492+49557470 Alt3
DPM1 ENSG00000000419-8-11,8-10-2/2 chr20:49557402-49557492 22 chr20:49558568,49557402-49557492+49557470 Alt3
C1orf112 ENSG00000000460-14-19,14-18-1/2 chr1:169773253-169773381 0 chr1:169772450,169773253+169773216-169773381 Alt3
")
parsed <- parseVastToolsEvent(events)
expect_is(parsed, "data.frame")
expect_equal(nrow(parsed), 3)
expect_equal(parsed$Program[[1]], "VAST-TOOLS")
expect_equal(parsed$C1.end[[1]], 49558568)
expect_equal(parsed$A1.start[[1]], 49557492)
expect_equal(parsed$A2.start[[1]], 49557470)
expect_equal(parsed$A2.end[[1]], 49557402)
expect_equal(parsed$Event.type[[1]], "A3SS")
expect_equal(parsed$Strand[[1]], "-")
expect_equal(parsed$C1.end[[2]], 49558568)
expect_equal(parsed$A1.start[[2]], 49557492)
expect_equal(parsed$A2.start[[2]], 49557470)
expect_equal(parsed$A2.end[[2]], 49557402)
expect_equal(parsed$Event.type[[2]], "A3SS")
expect_equal(parsed$Strand[[2]], "-")
expect_equal(parsed$C1.end[[3]], 169772450)
expect_equal(parsed$A1.start[[3]], 169773253)
expect_equal(parsed$A2.start[[3]], 169773216)
expect_equal(parsed$A2.end[[3]], 169773381)
expect_equal(parsed$Event.type[[3]], "A3SS")
expect_equal(parsed$Strand[[3]], "+")
})
test_that("parseVastToolsEvent parses alt. 3' splice site annotation with information missing", {
events <- read.table(
text = "DPM1 ENSG00000000419-8-11,8-10-1/2 chr20:49557402-49557470 0 chr20:49558568,-49557492+49557470 Alt3
DPM1 ENSG00000000419-8-11,8-10-2/2 chr20:49557402-49557492 22 chr20:49558568,-49557492+49557470 Alt3
C1orf112 ENSG00000000460-14-19,14-18-1/2 chr1:169773253-169773381 0 chr1:169772450,169773253+169773216- Alt3")
parsed <- parseVastToolsEvent(events)
expect_is(parsed, "data.frame")
expect_equal(nrow(parsed), 3)
expect_equal(parsed$Program[[1]], "VAST-TOOLS")
expect_equal(parsed$C1.end[[1]], 49558568)
expect_equal(parsed$A1.start[[1]], 49557492)
expect_equal(parsed$A2.start[[1]], 49557470)
expect_true(is.na(parsed$A2.end[[1]]))
expect_equal(parsed$Event.type[[1]], "A3SS")
expect_equal(parsed$Strand[[1]], "-")
expect_equal(parsed$C1.end[[2]], 49558568)
expect_equal(parsed$A1.start[[2]], 49557492)
expect_equal(parsed$A2.start[[2]], 49557470)
expect_true(is.na(parsed$A2.end[[2]]))
expect_equal(parsed$Event.type[[2]], "A3SS")
expect_equal(parsed$Strand[[2]], "-")
expect_equal(parsed$C1.end[[3]], 169772450)
expect_equal(parsed$A1.start[[3]], 169773253)
expect_equal(parsed$A2.start[[3]], 169773216)
expect_true(is.na(parsed$A2.end[[3]]))
expect_equal(parsed$Event.type[[3]], "A3SS")
expect_equal(parsed$Strand[[3]], "+")
})
test_that("parseVastToolsEvent parses alt. 5' splice site annotation", {
events <- read.table(
text = "
TSPAN6 ENSG00000000003-2-4,3-4-1/2 chrX:99891605-99891686 0 chrX:99891605+99891188-99891686,99890743 Alt5
DPM1 ENSG00000000419-9-11,10-11-1/2 chr20:49557666-49557746 0 chr20:49557666+49557642-49557746,49557470 Alt5
NFYA ENSG00000001167-3-4,4-4-1/2 chr6:41048553-41048633 0 chr6:41048553-41048633+41048636,41051785 Alt5
")
parsed <- parseVastToolsEvent(events)
expect_is(parsed, "data.frame")
expect_equal(nrow(parsed), 3)
expect_equal(parsed$Program[[1]], "VAST-TOOLS")
expect_equal(parsed$A2.start[[1]], 99891686)
expect_equal(parsed$A2.end[[1]], 99891188)
expect_equal(parsed$A1.end[[1]], 99891605)
expect_equal(parsed$C2.start[[1]], 99890743)
expect_equal(parsed$Event.type[[1]], "A5SS")
expect_equal(parsed$Strand[[1]], "-")
expect_equal(parsed$A2.start[[2]], 49557746)
expect_equal(parsed$A2.end[[2]], 49557642)
expect_equal(parsed$A1.end[[2]], 49557666)
expect_equal(parsed$C2.start[[2]], 49557470)
expect_equal(parsed$Event.type[[2]], "A5SS")
expect_equal(parsed$Strand[[2]], "-")
expect_equal(parsed$A2.start[[3]], 41048553)
expect_equal(parsed$A2.end[[3]], 41048636)
expect_equal(parsed$A1.end[[3]], 41048633)
expect_equal(parsed$C2.start[[3]], 41051785)
expect_equal(parsed$Event.type[[3]], "A5SS")
expect_equal(parsed$Strand[[3]], "+")
})
test_that("parseVastToolsEvent parses alt. 5' splice site annotation with information missing", {
events <- read.table(
text = "
TSPAN6 ENSG00000000003-2-4,3-4-1/2 chrX:99891605-99891686 0 chrX:99891605+99891188-,99890743 Alt5
DPM1 ENSG00000000419-9-11,10-11-1/2 chr20:49557666-49557746 0 chr20:49557666+49557642-,49557470 Alt5
NFYA ENSG00000001167-3-4,4-4-1/2 chr6:41048553-41048633 0 chr6:-41048633+41048636,41051785 Alt5
")
parsed <- parseVastToolsEvent(events)
expect_is(parsed, "data.frame")
expect_equal(nrow(parsed), 3)
expect_equal(parsed$Program[[1]], "VAST-TOOLS")
expect_true(is.na(parsed$A2.start[[1]]))
expect_equal(parsed$A2.end[[1]], 99891188)
expect_equal(parsed$A1.end[[1]], 99891605)
expect_equal(parsed$C2.start[[1]], 99890743)
expect_equal(parsed$Event.type[[1]], "A5SS")
expect_equal(parsed$Strand[[1]], "-")
expect_true(is.na(parsed$A2.start[[2]]))
expect_equal(parsed$A2.end[[2]], 49557642)
expect_equal(parsed$A1.end[[2]], 49557666)
expect_equal(parsed$C2.start[[2]], 49557470)
expect_equal(parsed$Event.type[[2]], "A5SS")
expect_equal(parsed$Strand[[2]], "-")
expect_true(is.na(parsed$A2.start[[3]]))
expect_equal(parsed$A2.end[[3]], 41048636)
expect_equal(parsed$A1.end[[3]], 41048633)
expect_equal(parsed$C2.start[[3]], 41051785)
expect_equal(parsed$Event.type[[3]], "A5SS")
expect_equal(parsed$Strand[[3]], "+")
})
test_that("parseVastToolsEvent parses retained intron annotation", {
events <- read.table(
text = "
A2M ENSG00000175899-A2M:NM_000014:9 chr12:9258942-9259086 145 chr12:9259087-9259201=9258832-9258941:- IR-S A2M:NM_000014:9
A2ML1 ENSG00000166535-A2ML1:NM_144670:1 chr12:8975310-8975777 468 chr12:8975150-8975309=8975778-8975961:+ IR-S A2ML1:NM_144670:1
A2ML1 ENSG00000166535-A2ML1:NM_144670:10 chr12:8991819-8993964 2146 chr12:8991709-8991818=8993965-8994132:+ IR-S A2ML1:NM_144670:10
")
parsed <- parseVastToolsEvent(events)
expect_is(parsed, "data.frame")
expect_equal(nrow(parsed), 3)
expect_equal(parsed$Program[[1]], "VAST-TOOLS")
expect_equal(parsed$C1.start[[1]], 9259201)
expect_equal(parsed$C1.end[[1]], 9259087)
expect_equal(parsed$C2.start[[1]], 9258941)
expect_equal(parsed$C2.end[[1]], 9258832)
expect_equal(parsed$Event.type[[1]], "RI")
expect_equal(parsed$Strand[[1]], "-")
expect_equal(parsed$C1.start[[2]], 8975150)
expect_equal(parsed$C1.end[[2]], 8975309)
expect_equal(parsed$C2.start[[2]], 8975778)
expect_equal(parsed$C2.end[[2]], 8975961)
expect_equal(parsed$Event.type[[2]], "RI")
expect_equal(parsed$Strand[[2]], "+")
expect_equal(parsed$C1.start[[3]], 8991709)
expect_equal(parsed$C1.end[[3]], 8991818)
expect_equal(parsed$C2.start[[3]], 8993965)
expect_equal(parsed$C2.end[[3]], 8994132)
expect_equal(parsed$Event.type[[3]], "RI")
expect_equal(parsed$Strand[[3]], "+")
})
test_that("parseVastToolsSE parses exon skipping junctions", {
junctions <- read.table(
text = "
169768099 169770024 169770112 169771762
99887482 99885756 99885863 99884983
")
parsed <- parseVastToolsSE(junctions)
expect_equal(parsed$Strand[[1]], "+")
expect_equal(parsed$C1.end[[1]], 169768099)
expect_equal(parsed$A1.start[[1]], 169770024)
expect_equal(parsed$A1.end[[1]], 169770112)
expect_equal(parsed$C2.start[[1]], 169771762)
expect_equal(parsed$Strand[[2]], "-")
expect_equal(parsed$C1.end[[2]], 99887482)
expect_equal(parsed$A1.start[[2]], 99885863)
expect_equal(parsed$A1.end[[2]], 99885756)
expect_equal(parsed$C2.start[[2]], 99884983)
})
test_that("parseVastToolsRI parses retained intron junctions", {
junctions <- read.table(
text = "
125549925 125550263 125558422 125558525
58864658 58864693 58864294 58864563
")
parsed <- parseVastToolsRI(junctions, c("+", "-"))
expect_equal(parsed$Strand[[1]], "+")
expect_equal(parsed$C1.start[[1]], 125549925)
expect_equal(parsed$C1.end[[1]], 125550263)
expect_equal(parsed$C2.start[[1]], 125558422)
expect_equal(parsed$C2.end[[1]], 125558525)
expect_equal(parsed$Strand[[2]], "-")
expect_equal(parsed$C1.start[[2]], 58864693)
expect_equal(parsed$C1.end[[2]], 58864658)
expect_equal(parsed$C2.start[[2]], 58864563)
expect_equal(parsed$C2.end[[2]], 58864294)
})
test_that("parseVastToolsA3SS parses alt. 3' splice site junctions", {
junctions <- rbind(
c(36276385, list(c(36277798, 36277315)), 36277974),
c(7133604, 7133377, list(c(7133474, 7133456)))
)
parsed <- parseVastToolsA3SS(junctions)
expect_equal(parsed$Strand[[1]], "+")
expect_equal(parsed$C1.end[[1]], 36276385)
expect_equal(parsed$A1.start[[1]], 36277798)
expect_equal(parsed$A2.start[[1]], 36277315)
expect_equal(parsed$A2.end[[1]], 36277974)
expect_equal(parsed$Strand[[2]], "-")
expect_equal(parsed$C1.end[[2]], 7133604)
expect_equal(parsed$A1.start[[2]], 7133474)
expect_equal(parsed$A2.start[[2]], 7133456)
expect_equal(parsed$A2.end[[2]], 7133377)
})
test_that("parseVastToolsA5SS parses alt. 5' splice site junctions", {
junctions <- rbind(
c(74650610, list(c(74650654, 74650658)), 74650982),
c(list(c(49557666, 49557642), 49557746, 49557470))
)
parsed <- parseVastToolsA5SS(junctions)
expect_equal(parsed$Strand, c("+", "-"))
# Plus strand
expect_equal(parsed$A2.start[[1]], 74650610)
expect_equal(parsed$A2.end[[1]], 74650658)
expect_equal(parsed$A1.end[[1]], 74650654)
expect_equal(parsed$C2.start[[1]], 74650982)
# Minus strand
expect_equal(parsed$A2.start[[2]], 49557746)
expect_equal(parsed$A2.end[[2]], 49557642)
expect_equal(parsed$A1.end[[2]], 49557666)
expect_equal(parsed$C2.start[[2]], 49557470)
})
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