tests/testthat/testMatsEvents.R
In nuno-agostinho/psichomics: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
context("Parse MATS splicing events")
test_that("parseMatsAnnotation parses annotation from rMATS", {
folder <- "extdata/eventsAnnotSample/mats_output/ASEvents"
matsOutput <- system.file(folder, package="psichomics")
mats <- parseMatsAnnotation(matsOutput)
expect_equal(nrow(mats), 83)
expect_is(mats, "ASevents")
expect_equal(length(mats), 14)
expect_equal(colnames(mats),
c("Program", "Gene", "Chromosome", "Strand", "Event.type",
"Event.ID", "C1.start", "C1.end", "A1.start", "A1.end",
"A2.start", "A2.end", "C2.start", "C2.end"))
expect_equal(unique(mats$Program), "MATS")
expect_equal(unique(mats$Strand), c("-", "+"))
# Do not parse novel events
mats <- parseMatsAnnotation(matsOutput, novelEvents=FALSE)
expect_equal(nrow(mats), 63)
expect_is(mats, "ASevents")
expect_equal(length(mats), 14)
expect_equal(colnames(mats),
c("Program", "Gene", "Chromosome", "Strand", "Event.type",
"Event.ID", "C1.start", "C1.end", "A1.start", "A1.end",
"A2.start", "A2.end", "C2.start", "C2.end"))
expect_equal(unique(mats$Program), "MATS")
expect_equal(unique(mats$Strand), c("-", "+"))
})
test_that("parseMatsEvent parses alt. 3' splice site events", {
event <- read.table(text = "
3658 ENSG00000067715 SYT1 chr12 + 79685787 79685910 79685796 79685910 79679566 79679751 3658 252 102 73 16 58 56 0.0342916452301 0.274333161841 0.705 0.815 -0.11
1234 ENSG00000076108 BAZ2A chr12 - 57000030 57000179 57000030 57000096 57000416 57000517 1234 0 18 2 0 112 56 0.00337999081157 0.0540798529851 0 1 -1
")
parsed <- parseMatsEvent(event, "A3SS")
expect_is(parsed, "data.frame")
# Plus strand
expect_equal(parsed[1, "Strand"], "+")
expect_equal(parsed[1, "C1.start"], 79679566)
expect_equal(parsed[1, "C1.end"], 79679751)
expect_equal(parsed[1, "A1.start"], 79685787)
expect_equal(parsed[1, "A2.start"], 79685796)
expect_equal(parsed[1, "A2.end"], 79685910)
expect_equal(parsed[1, "P.value"], 0.0342916452301)
expect_equal(parsed[1, "FDR"], 0.274333161841)
expect_equal(parsed[1, "Inclusion.level.A"], 0.705)
expect_equal(parsed[1, "Inclusion.level.B"], 0.815)
# Minus strand
expect_equal(parsed[2, "Strand"], "-")
expect_equal(parsed[2, "C1.start"], 57000517)
expect_equal(parsed[2, "C1.end"], 57000416)
expect_equal(parsed[2, "A1.start"], 57000179)
expect_equal(parsed[2, "A2.start"], 57000096)
expect_equal(parsed[2, "A2.end"], 57000030)
expect_equal(parsed[2, "P.value"], 0.00337999081157)
expect_equal(parsed[2, "FDR"], 0.0540798529851)
expect_equal(parsed[2, "Inclusion.level.A"], 0)
expect_equal(parsed[2, "Inclusion.level.B"], 1)
})
test_that("parseMatsEvent parses alt. 3' splice site event annotation", {
event <- read.table(text = "
1234 ENSG00000076108 BAZ2A chr12 - 57000030 57000179 57000030 57000096 57000416 57000517
")
parsed <- parseMatsEvent(event, "A3SS")
expect_is(parsed, "data.frame")
expect_equal(parsed$Strand, "-")
expect_equal(parsed$C1.start, 57000517)
expect_equal(parsed$C1.end, 57000416)
expect_equal(parsed$A1.start, 57000179)
expect_equal(parsed$A2.start, 57000096)
expect_equal(parsed$A2.end, 57000030)
})
test_that("parseMatsEvent parses alt. 5' splice events", {
event <- read.table(text = "
1366 ENSG00000172465 TCEAL1 chrX + 102884421 102884501 102884421 102884489 102884812 102885881 1366 2 2 1 0 61 56 0.489673743698 0.498132777769 0.479 1 -0.521
4064 ENSG00000077782 FGFR1 chr8 - 38285863 38285953 38285869 38285953 38285438 38285611 4064 2 1 1 3 56 56 0.344797594489 0.498132777769 0.667 0.25 0.417
")
parsed <- parseMatsEvent(event, "A5SS")
expect_is(parsed, "data.frame")
# Plus strand
expect_equal(parsed[1, "Strand"], "+")
expect_equal(parsed[1, "A2.start"], 102884421)
expect_equal(parsed[1, "A2.end"], 102884489)
expect_equal(parsed[1, "A1.end"], 102884501)
expect_equal(parsed[1, "C2.start"], 102884812)
expect_equal(parsed[1, "C2.end"], 102885881)
expect_equal(parsed[1, "P.value"], 0.489673743698)
expect_equal(parsed[1, "FDR"], 0.498132777769)
expect_equal(parsed[1, "Inclusion.level.A"], 0.479)
expect_equal(parsed[1, "Inclusion.level.B"], 1)
# Minus strand
expect_equal(parsed[2, "Strand"], "-")
expect_equal(parsed[2, "A2.start"], 38285953)
expect_equal(parsed[2, "A2.end"], 38285869)
expect_equal(parsed[2, "A1.end"], 38285863)
expect_equal(parsed[2, "C2.start"], 38285611)
expect_equal(parsed[2, "C2.end"], 38285438)
expect_equal(parsed[2, "P.value"], 0.344797594489)
expect_equal(parsed[2, "FDR"], 0.498132777769)
expect_equal(parsed[2, "Inclusion.level.A"], 0.667)
expect_equal(parsed[2, "Inclusion.level.B"], 0.25)
})
test_that("parseMatsEvent parses alt. 5' splice event annotation", {
event <- read.table(text = "
4064 ENSG00000077782 FGFR1 chr8 - 38285863 38285953 38285869 38285953 38285438 38285611
")
parsed <- parseMatsEvent(event, "A5SS")
expect_is(parsed, "data.frame")
expect_equal(parsed$Strand, "-")
expect_equal(parsed$A2.start, 38285953)
expect_equal(parsed$A2.end, 38285869)
expect_equal(parsed$A1.end, 38285863)
expect_equal(parsed$C2.start, 38285611)
expect_equal(parsed$C2.end, 38285438)
expect_null(parsed$P.value)
expect_null(parsed$FDR)
expect_null(parsed$Inclusion.level.A)
expect_null(parsed$Inclusion.level.B)
})
test_that("parseMatsEvent parses exon skipping events", {
event <- read.table(text = "
4626 ENSG00000151422 FER chr5 + 108168470 108168644 108133824 108134090 108171408 108171508 4626 16 0 0 4 112 56 0.000164083368228 0.0164083368228 1 0 1
16170 ENSG00000151914 DST chr6 - 56463273 56463507 56462537 56462804 56464866 56465019 16170 53 7 64 2 112 56 0.062949258326 0.796580100354 0.791 0.941 -0.15
")
event <- as.data.frame(rbind(event, deparse.level=FALSE))
parsed <- parseMatsEvent(event, "SE")
expect_is(parsed, "data.frame")
# Plus strand
expect_equal(parsed[1, "Strand"], "+")
expect_equal(parsed[1, "C1.start"], 108133824)
expect_equal(parsed[1, "C1.end"], 108134090)
expect_equal(parsed[1, "A1.start"], 108168470)
expect_equal(parsed[1, "A1.end"], 108168644)
expect_equal(parsed[1, "C2.start"], 108171408)
expect_equal(parsed[1, "C2.end"], 108171508)
expect_equal(parsed[1, "P.value"], 0.000164083368228)
expect_equal(parsed[1, "FDR"], 0.0164083368228)
expect_equal(parsed[1, "Inclusion.level.A"], 1)
expect_equal(parsed[1, "Inclusion.level.B"], 0)
# Minus strand
expect_equal(parsed[2, "Strand"], "-")
expect_equal(parsed[2, "C1.start"], 56465019)
expect_equal(parsed[2, "C1.end"], 56464866)
expect_equal(parsed[2, "A1.start"], 56463507)
expect_equal(parsed[2, "A1.end"], 56463273)
expect_equal(parsed[2, "C2.start"], 56462804)
expect_equal(parsed[2, "C2.end"], 56462537)
expect_equal(parsed[2, "P.value"], 0.062949258326)
expect_equal(parsed[2, "FDR"], 0.796580100354)
expect_equal(parsed[2, "Inclusion.level.A"], 0.791)
expect_equal(parsed[2, "Inclusion.level.B"], 0.941)
})
test_that("parseMatsEvent parses exon skipping event annotation", {
event <- read.table(text = "
16170 ENSG00000151914 DST chr6 - 56463273 56463507 56462537 56462804 56464866 56465019
")
parsed <- parseMatsEvent(event, "SE")
expect_is(parsed, "data.frame")
expect_equal(parsed$Strand, "-")
expect_equal(parsed$C1.start, 56465019)
expect_equal(parsed$C1.end, 56464866)
expect_equal(parsed$A1.start, 56463507)
expect_equal(parsed$A1.end, 56463273)
expect_equal(parsed$C2.start, 56462804)
expect_equal(parsed$C2.end, 56462537)
expect_null(parsed$P.value)
expect_null(parsed$FDR)
expect_null(parsed$Inclusion.level.A)
expect_null(parsed$Inclusion.level.B)
})
test_that("parseMatsEvent parses retained intron events", {
event <- read.table(text = "
2287 ENSG00000011295 TTC19 chr17 + 15929853 15932100 15929853 15930016 15930687 15932100 2287 0 4 1 0 112 56 0.122321609511 0.842461398441 0 1 -1
1324 ENSG00000121851 POLR3GL chr1 - 145456990 145457309 145456990 145457104 145457235 145457309 1324 1 12 0 5 112 56 0.588614424316 0.920102552754 0.04 0 0.04
")
parsed <- parseMatsEvent(event, "RI")
expect_is(parsed, "data.frame")
# Plus strand
expect_equal(parsed[1, "Strand"], "+")
expect_equal(parsed[1, "C1.start"], 15929853)
expect_equal(parsed[1, "C1.end"], 15930016)
expect_equal(parsed[1, "C2.start"], 15930687)
expect_equal(parsed[1, "C2.end"], 15932100)
expect_equal(parsed[1, "P.value"], 0.122321609511)
expect_equal(parsed[1, "FDR"], 0.842461398441)
expect_equal(parsed[1, "Inclusion.level.A"], 0)
expect_equal(parsed[1, "Inclusion.level.B"], 1)
# Minus strand
expect_equal(parsed[2, "Strand"], "-")
expect_equal(parsed[2, "C1.start"], 145457309)
expect_equal(parsed[2, "C1.end"], 145457235)
expect_equal(parsed[2, "C2.start"], 145457104)
expect_equal(parsed[2, "C2.end"], 145456990)
expect_equal(parsed[2, "P.value"], 0.588614424316)
expect_equal(parsed[2, "FDR"], 0.920102552754)
expect_equal(parsed[2, "Inclusion.level.A"], 0.04)
expect_equal(parsed[2, "Inclusion.level.B"], 0)
})
test_that("parseMatsEvent parses retained intron event annotation", {
event <- read.table(text = "
1324 ENSG00000121851 POLR3GL chr1 - 145456990 145457309 145456990 145457104 145457235 145457309
")
parsed <- parseMatsEvent(event, "RI")
expect_is(parsed, "data.frame")
expect_equal(parsed$Strand, "-")
expect_equal(parsed$C1.start, 145457309)
expect_equal(parsed$C1.end, 145457235)
expect_equal(parsed$C2.start, 145457104)
expect_equal(parsed$C2.end, 145456990)
expect_null(parsed$P.value)
expect_null(parsed$FDR)
expect_null(parsed$Inclusion.level.A)
expect_null(parsed$Inclusion.level.B)
})
test_that("parseMatsEvent parses mutually exc. exons events", {
event <- read.table(text = "
217 ENSG00000120251 GRIA2 chr4 + 158282161 158282276 158282689 158282804 158281047 158281295 158283950 158284199 217 10 0 7 1 112 112 0.321107675238 0.559168057922 1 0.875 0.125
1388 ENSG00000138468 SENP7 chr3 - 101117704 101117899 101136436 101136634 101090851 101090970 101177798 101177896 1388 0 5 1 3 112 112 0.327510084993 0.559168057922 0 0.25 -0.25
")
parsed <- parseMatsEvent(event, "MXE")
expect_is(parsed, "data.frame")
# Plus strand
expect_equal(parsed[1, "Strand"], "+")
expect_equal(parsed[1, "C1.start"], 158281047)
expect_equal(parsed[1, "C1.end"], 158281295)
expect_equal(parsed[1, "A1.start"], 158282161)
expect_equal(parsed[1, "A1.end"], 158282276)
expect_equal(parsed[1, "A2.start"], 158282689)
expect_equal(parsed[1, "A2.end"], 158282804)
expect_equal(parsed[1, "C2.start"], 158283950)
expect_equal(parsed[1, "C2.end"], 158284199)
expect_equal(parsed[1, "P.value"], 0.321107675238)
expect_equal(parsed[1, "FDR"], 0.559168057922)
expect_equal(parsed[1, "Inclusion.level.A"], 1)
expect_equal(parsed[1, "Inclusion.level.B"], 0.875)
# Minus strand
expect_equal(parsed[2, "Strand"], "-")
expect_equal(parsed[2, "C1.start"], 101177896)
expect_equal(parsed[2, "C1.end"], 101177798)
expect_equal(parsed[2, "A1.start"], 101117899)
expect_equal(parsed[2, "A1.end"], 101117704)
expect_equal(parsed[2, "A2.start"], 101136634)
expect_equal(parsed[2, "A2.end"], 101136436)
expect_equal(parsed[2, "C2.start"], 101090970)
expect_equal(parsed[2, "C2.end"], 101090851)
expect_equal(parsed[2, "P.value"], 0.327510084993)
expect_equal(parsed[2, "FDR"], 0.559168057922)
expect_equal(parsed[2, "Inclusion.level.A"], 0)
expect_equal(parsed[2, "Inclusion.level.B"], 0.25)
})
test_that("parseMatsEvent parses mutually exc. exons event annotation", {
event <- read.table(text = "
1388 ENSG00000138468 SENP7 chr3 - 101117704 101117899 101136436 101136634 101090851 101090970 101177798 101177896
")
parsed <- parseMatsEvent(event, "MXE")
expect_is(parsed, "data.frame")
expect_equal(parsed$Strand, "-")
expect_equal(parsed$C1.start, 101177896)
expect_equal(parsed$C1.end, 101177798)
expect_equal(parsed$A1.start, 101117899)
expect_equal(parsed$A1.end, 101117704)
expect_equal(parsed$A2.start, 101136634)
expect_equal(parsed$A2.end, 101136436)
expect_equal(parsed$C2.start, 101090970)
expect_equal(parsed$C2.end, 101090851)
expect_null(parsed$P.value)
expect_null(parsed$FDR)
expect_null(parsed$Inclusion.level.A)
expect_null(parsed$Inclusion.level.B)
})
test_that("parseMatsEvent parses alt. first exon event annotation", {
event <- read.table(text = "
54 ENSG00000072958 AP1M1 chr19 + 16308723 16308879 16308967 16309119 16314269 16314426
1 ENSG00000007372 PAX6 chr11 - 31839356 31839483 31822086 31822194 31816177 31816336
")
parsed <- parseMatsEvent(event, "AFE")
expect_is(parsed, "data.frame")
# Plus strand
expect_equal(parsed[1, "Strand"], "+")
expect_equal(parsed[1, "A2.start"], 16308967)
expect_equal(parsed[1, "A2.end"], 16309119)
expect_equal(parsed[1, "A1.start"], 16308723)
expect_equal(parsed[1, "A1.end"], 16308879)
expect_equal(parsed[1, "C2.start"], 16314269)
expect_equal(parsed[1, "C2.end"], 16314426)
expect_null(parsed[1, "P.value"])
expect_null(parsed[1, "FDR"])
expect_null(parsed[1, "Inclusion.level.A"])
expect_null(parsed[1, "Inclusion.level.B"])
# Minus strand
expect_equal(parsed[2, "Strand"], "-")
expect_equal(parsed[2, "A2.start"], 31822194)
expect_equal(parsed[2, "A2.end"], 31822086)
expect_equal(parsed[2, "A1.start"], 31839483)
expect_equal(parsed[2, "A1.end"], 31839356)
expect_equal(parsed[2, "C2.start"], 31816336)
expect_equal(parsed[2, "C2.end"], 31816177)
expect_null(parsed[2, "P.value"])
expect_null(parsed[2, "FDR"])
expect_null(parsed[2, "Inclusion.level.A"])
expect_null(parsed[2, "Inclusion.level.B"])
})
test_that("parseMatsEvent parses alt. last exon event annotation", {
event <- read.table(text = "
14 ENSG00000153093 ACOXL chr2 + 111858645 111858828 111851063 111851921 111850441 111850543
32 ENSG00000223745 RP4-717I23.3 chr1 - 93770667 93771027 93776725 93777165 93790191 93790286
")
parsed <- parseMatsEvent(event, "ALE")
expect_is(parsed, "data.frame")
# Plus strand
expect_equal(parsed[1, "Strand"], "+")
expect_equal(parsed[1, "C1.start"], 111850441)
expect_equal(parsed[1, "C1.end"], 111850543)
expect_equal(parsed[1, "A1.start"], 111851063)
expect_equal(parsed[1, "A1.end"], 111851921)
expect_equal(parsed[1, "A2.start"], 111858645)
expect_equal(parsed[1, "A2.end"], 111858828)
expect_null(parsed[1, "P.value"])
expect_null(parsed[1, "FDR"])
expect_null(parsed[1, "Inclusion.level.A"])
expect_null(parsed[1, "Inclusion.level.B"])
# Minus strand
expect_equal(parsed[2, "C1.start"], 93790286)
expect_equal(parsed[2, "C1.end"], 93790191)
expect_equal(parsed[2, "A1.start"], 93777165)
expect_equal(parsed[2, "A1.end"], 93776725)
expect_equal(parsed[2, "A2.start"], 93771027)
expect_equal(parsed[2, "A2.end"], 93770667)
expect_null(parsed[2, "P.value"])
expect_null(parsed[2, "FDR"])
expect_null(parsed[2, "Inclusion.level.A"])
expect_null(parsed[2, "Inclusion.level.B"])
})
test_that("parseMatsSE parses a exon skipping event's junctions", {
junctions <- read.table(
text = "79685787 79685910 79685796 79685910 79679566 79679751")
parsed <- parseMatsSE(junctions, strand = "+")
expect_equal(parsed$C1.start, 79685796)
expect_equal(parsed$C1.end, 79685910)
expect_equal(parsed$A1.start, 79685787)
expect_equal(parsed$A1.end, 79685910)
expect_equal(parsed$C2.start, 79679566)
expect_equal(parsed$C2.end, 79679751)
})
test_that("parseMatsMXE parses a mutually exclusive exon event's junctions", {
junctions <- read.table(
text= "158282161 158282276 158282689 158282804 158281047 158281295 158283950 158284199")
parsed <- parseMatsMXE(junctions, strand = "+")
expect_equal(parsed$C1.start, 158281047)
expect_equal(parsed$C1.end, 158281295)
expect_equal(parsed$A1.start, 158282161)
expect_equal(parsed$A1.end, 158282276)
expect_equal(parsed$A2.start, 158282689)
expect_equal(parsed$A2.end, 158282804)
expect_equal(parsed$C2.start, 158283950)
expect_equal(parsed$C2.end, 158284199)
})
test_that("parseMatsRI parses a retained intron event's junctions", {
junctions <- read.table(
text = "15929853 15932100 15929853 15930016 15930687 15932100")
parsed <- parseMatsRI(junctions, strand = "+")
expect_equal(parsed$C1.start, 15929853)
expect_equal(parsed$C1.end, 15930016)
expect_equal(parsed$C2.start, 15930687)
expect_equal(parsed$C2.end, 15932100)
})
test_that("parseMatsA3SS parses an alt. 3' splice site event's junctions", {
junctions <- read.table(
text = "79685787 79685910 79685796 79685910 79679566 79679751")
parsed <- parseMatsA3SS(junctions, strand = "+")
expect_equal(parsed$C1.start, 79679566)
expect_equal(parsed$C1.end, 79679751)
expect_equal(parsed$A1.start, 79685787)
expect_equal(parsed$A2.start, 79685796)
expect_equal(parsed$A2.end, 79685910)
})
test_that("parseMatsA3SS parses an alt. 5' splice site event's junctions", {
junctions <- read.table(
text="102884421 102884501 102884421 102884489 102884812 102885881")
parsed <- parseMatsA5SS(junctions, strand = "+")
expect_equal(parsed$A2.start, 102884421)
expect_equal(parsed$A2.end, 102884489)
expect_equal(parsed$A1.end, 102884501)
expect_equal(parsed$C2.start, 102884812)
expect_equal(parsed$C2.end, 102885881)
})
test_that("parseMatsAFE parses an alt. first exon event's junctions", {
junctions <- read.table(
text = "16308723 16308879 16308967 16309119 16314269 16314426")
parsed <- parseMatsAFE(junctions, strand = "+")
expect_equal(parsed$A2.start, 16308967)
expect_equal(parsed$A2.end, 16309119)
expect_equal(parsed$A1.start, 16308723)
expect_equal(parsed$A1.end, 16308879)
expect_equal(parsed$C2.start, 16314269)
expect_equal(parsed$C2.end, 16314426)
})
test_that("parseMatsALE parses an alt. last exon event's junctions", {
junctions <- read.table(
text = "111858645 111858828 111851063 111851921 111850441 111850543")
parsed <- parseMatsALE(junctions, strand = "+")
expect_equal(parsed$C1.start, 111850441)
expect_equal(parsed$C1.end, 111850543)
expect_equal(parsed$A1.start, 111851063)
expect_equal(parsed$A1.end, 111851921)
expect_equal(parsed$A2.start, 111858645)
expect_equal(parsed$A2.end, 111858828)
})
nuno-agostinho/psichomics documentation built on Feb. 11, 2024, 11:16 p.m.
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context("Parse MATS splicing events")
test_that("parseMatsAnnotation parses annotation from rMATS", {
folder <- "extdata/eventsAnnotSample/mats_output/ASEvents"
matsOutput <- system.file(folder, package="psichomics")
mats <- parseMatsAnnotation(matsOutput)
expect_equal(nrow(mats), 83)
expect_is(mats, "ASevents")
expect_equal(length(mats), 14)
expect_equal(colnames(mats),
c("Program", "Gene", "Chromosome", "Strand", "Event.type",
"Event.ID", "C1.start", "C1.end", "A1.start", "A1.end",
"A2.start", "A2.end", "C2.start", "C2.end"))
expect_equal(unique(mats$Program), "MATS")
expect_equal(unique(mats$Strand), c("-", "+"))
# Do not parse novel events
mats <- parseMatsAnnotation(matsOutput, novelEvents=FALSE)
expect_equal(nrow(mats), 63)
expect_is(mats, "ASevents")
expect_equal(length(mats), 14)
expect_equal(colnames(mats),
c("Program", "Gene", "Chromosome", "Strand", "Event.type",
"Event.ID", "C1.start", "C1.end", "A1.start", "A1.end",
"A2.start", "A2.end", "C2.start", "C2.end"))
expect_equal(unique(mats$Program), "MATS")
expect_equal(unique(mats$Strand), c("-", "+"))
})
test_that("parseMatsEvent parses alt. 3' splice site events", {
event <- read.table(text = "
3658 ENSG00000067715 SYT1 chr12 + 79685787 79685910 79685796 79685910 79679566 79679751 3658 252 102 73 16 58 56 0.0342916452301 0.274333161841 0.705 0.815 -0.11
1234 ENSG00000076108 BAZ2A chr12 - 57000030 57000179 57000030 57000096 57000416 57000517 1234 0 18 2 0 112 56 0.00337999081157 0.0540798529851 0 1 -1
")
parsed <- parseMatsEvent(event, "A3SS")
expect_is(parsed, "data.frame")
# Plus strand
expect_equal(parsed[1, "Strand"], "+")
expect_equal(parsed[1, "C1.start"], 79679566)
expect_equal(parsed[1, "C1.end"], 79679751)
expect_equal(parsed[1, "A1.start"], 79685787)
expect_equal(parsed[1, "A2.start"], 79685796)
expect_equal(parsed[1, "A2.end"], 79685910)
expect_equal(parsed[1, "P.value"], 0.0342916452301)
expect_equal(parsed[1, "FDR"], 0.274333161841)
expect_equal(parsed[1, "Inclusion.level.A"], 0.705)
expect_equal(parsed[1, "Inclusion.level.B"], 0.815)
# Minus strand
expect_equal(parsed[2, "Strand"], "-")
expect_equal(parsed[2, "C1.start"], 57000517)
expect_equal(parsed[2, "C1.end"], 57000416)
expect_equal(parsed[2, "A1.start"], 57000179)
expect_equal(parsed[2, "A2.start"], 57000096)
expect_equal(parsed[2, "A2.end"], 57000030)
expect_equal(parsed[2, "P.value"], 0.00337999081157)
expect_equal(parsed[2, "FDR"], 0.0540798529851)
expect_equal(parsed[2, "Inclusion.level.A"], 0)
expect_equal(parsed[2, "Inclusion.level.B"], 1)
})
test_that("parseMatsEvent parses alt. 3' splice site event annotation", {
event <- read.table(text = "
1234 ENSG00000076108 BAZ2A chr12 - 57000030 57000179 57000030 57000096 57000416 57000517
")
parsed <- parseMatsEvent(event, "A3SS")
expect_is(parsed, "data.frame")
expect_equal(parsed$Strand, "-")
expect_equal(parsed$C1.start, 57000517)
expect_equal(parsed$C1.end, 57000416)
expect_equal(parsed$A1.start, 57000179)
expect_equal(parsed$A2.start, 57000096)
expect_equal(parsed$A2.end, 57000030)
})
test_that("parseMatsEvent parses alt. 5' splice events", {
event <- read.table(text = "
1366 ENSG00000172465 TCEAL1 chrX + 102884421 102884501 102884421 102884489 102884812 102885881 1366 2 2 1 0 61 56 0.489673743698 0.498132777769 0.479 1 -0.521
4064 ENSG00000077782 FGFR1 chr8 - 38285863 38285953 38285869 38285953 38285438 38285611 4064 2 1 1 3 56 56 0.344797594489 0.498132777769 0.667 0.25 0.417
")
parsed <- parseMatsEvent(event, "A5SS")
expect_is(parsed, "data.frame")
# Plus strand
expect_equal(parsed[1, "Strand"], "+")
expect_equal(parsed[1, "A2.start"], 102884421)
expect_equal(parsed[1, "A2.end"], 102884489)
expect_equal(parsed[1, "A1.end"], 102884501)
expect_equal(parsed[1, "C2.start"], 102884812)
expect_equal(parsed[1, "C2.end"], 102885881)
expect_equal(parsed[1, "P.value"], 0.489673743698)
expect_equal(parsed[1, "FDR"], 0.498132777769)
expect_equal(parsed[1, "Inclusion.level.A"], 0.479)
expect_equal(parsed[1, "Inclusion.level.B"], 1)
# Minus strand
expect_equal(parsed[2, "Strand"], "-")
expect_equal(parsed[2, "A2.start"], 38285953)
expect_equal(parsed[2, "A2.end"], 38285869)
expect_equal(parsed[2, "A1.end"], 38285863)
expect_equal(parsed[2, "C2.start"], 38285611)
expect_equal(parsed[2, "C2.end"], 38285438)
expect_equal(parsed[2, "P.value"], 0.344797594489)
expect_equal(parsed[2, "FDR"], 0.498132777769)
expect_equal(parsed[2, "Inclusion.level.A"], 0.667)
expect_equal(parsed[2, "Inclusion.level.B"], 0.25)
})
test_that("parseMatsEvent parses alt. 5' splice event annotation", {
event <- read.table(text = "
4064 ENSG00000077782 FGFR1 chr8 - 38285863 38285953 38285869 38285953 38285438 38285611
")
parsed <- parseMatsEvent(event, "A5SS")
expect_is(parsed, "data.frame")
expect_equal(parsed$Strand, "-")
expect_equal(parsed$A2.start, 38285953)
expect_equal(parsed$A2.end, 38285869)
expect_equal(parsed$A1.end, 38285863)
expect_equal(parsed$C2.start, 38285611)
expect_equal(parsed$C2.end, 38285438)
expect_null(parsed$P.value)
expect_null(parsed$FDR)
expect_null(parsed$Inclusion.level.A)
expect_null(parsed$Inclusion.level.B)
})
test_that("parseMatsEvent parses exon skipping events", {
event <- read.table(text = "
4626 ENSG00000151422 FER chr5 + 108168470 108168644 108133824 108134090 108171408 108171508 4626 16 0 0 4 112 56 0.000164083368228 0.0164083368228 1 0 1
16170 ENSG00000151914 DST chr6 - 56463273 56463507 56462537 56462804 56464866 56465019 16170 53 7 64 2 112 56 0.062949258326 0.796580100354 0.791 0.941 -0.15
")
event <- as.data.frame(rbind(event, deparse.level=FALSE))
parsed <- parseMatsEvent(event, "SE")
expect_is(parsed, "data.frame")
# Plus strand
expect_equal(parsed[1, "Strand"], "+")
expect_equal(parsed[1, "C1.start"], 108133824)
expect_equal(parsed[1, "C1.end"], 108134090)
expect_equal(parsed[1, "A1.start"], 108168470)
expect_equal(parsed[1, "A1.end"], 108168644)
expect_equal(parsed[1, "C2.start"], 108171408)
expect_equal(parsed[1, "C2.end"], 108171508)
expect_equal(parsed[1, "P.value"], 0.000164083368228)
expect_equal(parsed[1, "FDR"], 0.0164083368228)
expect_equal(parsed[1, "Inclusion.level.A"], 1)
expect_equal(parsed[1, "Inclusion.level.B"], 0)
# Minus strand
expect_equal(parsed[2, "Strand"], "-")
expect_equal(parsed[2, "C1.start"], 56465019)
expect_equal(parsed[2, "C1.end"], 56464866)
expect_equal(parsed[2, "A1.start"], 56463507)
expect_equal(parsed[2, "A1.end"], 56463273)
expect_equal(parsed[2, "C2.start"], 56462804)
expect_equal(parsed[2, "C2.end"], 56462537)
expect_equal(parsed[2, "P.value"], 0.062949258326)
expect_equal(parsed[2, "FDR"], 0.796580100354)
expect_equal(parsed[2, "Inclusion.level.A"], 0.791)
expect_equal(parsed[2, "Inclusion.level.B"], 0.941)
})
test_that("parseMatsEvent parses exon skipping event annotation", {
event <- read.table(text = "
16170 ENSG00000151914 DST chr6 - 56463273 56463507 56462537 56462804 56464866 56465019
")
parsed <- parseMatsEvent(event, "SE")
expect_is(parsed, "data.frame")
expect_equal(parsed$Strand, "-")
expect_equal(parsed$C1.start, 56465019)
expect_equal(parsed$C1.end, 56464866)
expect_equal(parsed$A1.start, 56463507)
expect_equal(parsed$A1.end, 56463273)
expect_equal(parsed$C2.start, 56462804)
expect_equal(parsed$C2.end, 56462537)
expect_null(parsed$P.value)
expect_null(parsed$FDR)
expect_null(parsed$Inclusion.level.A)
expect_null(parsed$Inclusion.level.B)
})
test_that("parseMatsEvent parses retained intron events", {
event <- read.table(text = "
2287 ENSG00000011295 TTC19 chr17 + 15929853 15932100 15929853 15930016 15930687 15932100 2287 0 4 1 0 112 56 0.122321609511 0.842461398441 0 1 -1
1324 ENSG00000121851 POLR3GL chr1 - 145456990 145457309 145456990 145457104 145457235 145457309 1324 1 12 0 5 112 56 0.588614424316 0.920102552754 0.04 0 0.04
")
parsed <- parseMatsEvent(event, "RI")
expect_is(parsed, "data.frame")
# Plus strand
expect_equal(parsed[1, "Strand"], "+")
expect_equal(parsed[1, "C1.start"], 15929853)
expect_equal(parsed[1, "C1.end"], 15930016)
expect_equal(parsed[1, "C2.start"], 15930687)
expect_equal(parsed[1, "C2.end"], 15932100)
expect_equal(parsed[1, "P.value"], 0.122321609511)
expect_equal(parsed[1, "FDR"], 0.842461398441)
expect_equal(parsed[1, "Inclusion.level.A"], 0)
expect_equal(parsed[1, "Inclusion.level.B"], 1)
# Minus strand
expect_equal(parsed[2, "Strand"], "-")
expect_equal(parsed[2, "C1.start"], 145457309)
expect_equal(parsed[2, "C1.end"], 145457235)
expect_equal(parsed[2, "C2.start"], 145457104)
expect_equal(parsed[2, "C2.end"], 145456990)
expect_equal(parsed[2, "P.value"], 0.588614424316)
expect_equal(parsed[2, "FDR"], 0.920102552754)
expect_equal(parsed[2, "Inclusion.level.A"], 0.04)
expect_equal(parsed[2, "Inclusion.level.B"], 0)
})
test_that("parseMatsEvent parses retained intron event annotation", {
event <- read.table(text = "
1324 ENSG00000121851 POLR3GL chr1 - 145456990 145457309 145456990 145457104 145457235 145457309
")
parsed <- parseMatsEvent(event, "RI")
expect_is(parsed, "data.frame")
expect_equal(parsed$Strand, "-")
expect_equal(parsed$C1.start, 145457309)
expect_equal(parsed$C1.end, 145457235)
expect_equal(parsed$C2.start, 145457104)
expect_equal(parsed$C2.end, 145456990)
expect_null(parsed$P.value)
expect_null(parsed$FDR)
expect_null(parsed$Inclusion.level.A)
expect_null(parsed$Inclusion.level.B)
})
test_that("parseMatsEvent parses mutually exc. exons events", {
event <- read.table(text = "
217 ENSG00000120251 GRIA2 chr4 + 158282161 158282276 158282689 158282804 158281047 158281295 158283950 158284199 217 10 0 7 1 112 112 0.321107675238 0.559168057922 1 0.875 0.125
1388 ENSG00000138468 SENP7 chr3 - 101117704 101117899 101136436 101136634 101090851 101090970 101177798 101177896 1388 0 5 1 3 112 112 0.327510084993 0.559168057922 0 0.25 -0.25
")
parsed <- parseMatsEvent(event, "MXE")
expect_is(parsed, "data.frame")
# Plus strand
expect_equal(parsed[1, "Strand"], "+")
expect_equal(parsed[1, "C1.start"], 158281047)
expect_equal(parsed[1, "C1.end"], 158281295)
expect_equal(parsed[1, "A1.start"], 158282161)
expect_equal(parsed[1, "A1.end"], 158282276)
expect_equal(parsed[1, "A2.start"], 158282689)
expect_equal(parsed[1, "A2.end"], 158282804)
expect_equal(parsed[1, "C2.start"], 158283950)
expect_equal(parsed[1, "C2.end"], 158284199)
expect_equal(parsed[1, "P.value"], 0.321107675238)
expect_equal(parsed[1, "FDR"], 0.559168057922)
expect_equal(parsed[1, "Inclusion.level.A"], 1)
expect_equal(parsed[1, "Inclusion.level.B"], 0.875)
# Minus strand
expect_equal(parsed[2, "Strand"], "-")
expect_equal(parsed[2, "C1.start"], 101177896)
expect_equal(parsed[2, "C1.end"], 101177798)
expect_equal(parsed[2, "A1.start"], 101117899)
expect_equal(parsed[2, "A1.end"], 101117704)
expect_equal(parsed[2, "A2.start"], 101136634)
expect_equal(parsed[2, "A2.end"], 101136436)
expect_equal(parsed[2, "C2.start"], 101090970)
expect_equal(parsed[2, "C2.end"], 101090851)
expect_equal(parsed[2, "P.value"], 0.327510084993)
expect_equal(parsed[2, "FDR"], 0.559168057922)
expect_equal(parsed[2, "Inclusion.level.A"], 0)
expect_equal(parsed[2, "Inclusion.level.B"], 0.25)
})
test_that("parseMatsEvent parses mutually exc. exons event annotation", {
event <- read.table(text = "
1388 ENSG00000138468 SENP7 chr3 - 101117704 101117899 101136436 101136634 101090851 101090970 101177798 101177896
")
parsed <- parseMatsEvent(event, "MXE")
expect_is(parsed, "data.frame")
expect_equal(parsed$Strand, "-")
expect_equal(parsed$C1.start, 101177896)
expect_equal(parsed$C1.end, 101177798)
expect_equal(parsed$A1.start, 101117899)
expect_equal(parsed$A1.end, 101117704)
expect_equal(parsed$A2.start, 101136634)
expect_equal(parsed$A2.end, 101136436)
expect_equal(parsed$C2.start, 101090970)
expect_equal(parsed$C2.end, 101090851)
expect_null(parsed$P.value)
expect_null(parsed$FDR)
expect_null(parsed$Inclusion.level.A)
expect_null(parsed$Inclusion.level.B)
})
test_that("parseMatsEvent parses alt. first exon event annotation", {
event <- read.table(text = "
54 ENSG00000072958 AP1M1 chr19 + 16308723 16308879 16308967 16309119 16314269 16314426
1 ENSG00000007372 PAX6 chr11 - 31839356 31839483 31822086 31822194 31816177 31816336
")
parsed <- parseMatsEvent(event, "AFE")
expect_is(parsed, "data.frame")
# Plus strand
expect_equal(parsed[1, "Strand"], "+")
expect_equal(parsed[1, "A2.start"], 16308967)
expect_equal(parsed[1, "A2.end"], 16309119)
expect_equal(parsed[1, "A1.start"], 16308723)
expect_equal(parsed[1, "A1.end"], 16308879)
expect_equal(parsed[1, "C2.start"], 16314269)
expect_equal(parsed[1, "C2.end"], 16314426)
expect_null(parsed[1, "P.value"])
expect_null(parsed[1, "FDR"])
expect_null(parsed[1, "Inclusion.level.A"])
expect_null(parsed[1, "Inclusion.level.B"])
# Minus strand
expect_equal(parsed[2, "Strand"], "-")
expect_equal(parsed[2, "A2.start"], 31822194)
expect_equal(parsed[2, "A2.end"], 31822086)
expect_equal(parsed[2, "A1.start"], 31839483)
expect_equal(parsed[2, "A1.end"], 31839356)
expect_equal(parsed[2, "C2.start"], 31816336)
expect_equal(parsed[2, "C2.end"], 31816177)
expect_null(parsed[2, "P.value"])
expect_null(parsed[2, "FDR"])
expect_null(parsed[2, "Inclusion.level.A"])
expect_null(parsed[2, "Inclusion.level.B"])
})
test_that("parseMatsEvent parses alt. last exon event annotation", {
event <- read.table(text = "
14 ENSG00000153093 ACOXL chr2 + 111858645 111858828 111851063 111851921 111850441 111850543
32 ENSG00000223745 RP4-717I23.3 chr1 - 93770667 93771027 93776725 93777165 93790191 93790286
")
parsed <- parseMatsEvent(event, "ALE")
expect_is(parsed, "data.frame")
# Plus strand
expect_equal(parsed[1, "Strand"], "+")
expect_equal(parsed[1, "C1.start"], 111850441)
expect_equal(parsed[1, "C1.end"], 111850543)
expect_equal(parsed[1, "A1.start"], 111851063)
expect_equal(parsed[1, "A1.end"], 111851921)
expect_equal(parsed[1, "A2.start"], 111858645)
expect_equal(parsed[1, "A2.end"], 111858828)
expect_null(parsed[1, "P.value"])
expect_null(parsed[1, "FDR"])
expect_null(parsed[1, "Inclusion.level.A"])
expect_null(parsed[1, "Inclusion.level.B"])
# Minus strand
expect_equal(parsed[2, "C1.start"], 93790286)
expect_equal(parsed[2, "C1.end"], 93790191)
expect_equal(parsed[2, "A1.start"], 93777165)
expect_equal(parsed[2, "A1.end"], 93776725)
expect_equal(parsed[2, "A2.start"], 93771027)
expect_equal(parsed[2, "A2.end"], 93770667)
expect_null(parsed[2, "P.value"])
expect_null(parsed[2, "FDR"])
expect_null(parsed[2, "Inclusion.level.A"])
expect_null(parsed[2, "Inclusion.level.B"])
})
test_that("parseMatsSE parses a exon skipping event's junctions", {
junctions <- read.table(
text = "79685787 79685910 79685796 79685910 79679566 79679751")
parsed <- parseMatsSE(junctions, strand = "+")
expect_equal(parsed$C1.start, 79685796)
expect_equal(parsed$C1.end, 79685910)
expect_equal(parsed$A1.start, 79685787)
expect_equal(parsed$A1.end, 79685910)
expect_equal(parsed$C2.start, 79679566)
expect_equal(parsed$C2.end, 79679751)
})
test_that("parseMatsMXE parses a mutually exclusive exon event's junctions", {
junctions <- read.table(
text= "158282161 158282276 158282689 158282804 158281047 158281295 158283950 158284199")
parsed <- parseMatsMXE(junctions, strand = "+")
expect_equal(parsed$C1.start, 158281047)
expect_equal(parsed$C1.end, 158281295)
expect_equal(parsed$A1.start, 158282161)
expect_equal(parsed$A1.end, 158282276)
expect_equal(parsed$A2.start, 158282689)
expect_equal(parsed$A2.end, 158282804)
expect_equal(parsed$C2.start, 158283950)
expect_equal(parsed$C2.end, 158284199)
})
test_that("parseMatsRI parses a retained intron event's junctions", {
junctions <- read.table(
text = "15929853 15932100 15929853 15930016 15930687 15932100")
parsed <- parseMatsRI(junctions, strand = "+")
expect_equal(parsed$C1.start, 15929853)
expect_equal(parsed$C1.end, 15930016)
expect_equal(parsed$C2.start, 15930687)
expect_equal(parsed$C2.end, 15932100)
})
test_that("parseMatsA3SS parses an alt. 3' splice site event's junctions", {
junctions <- read.table(
text = "79685787 79685910 79685796 79685910 79679566 79679751")
parsed <- parseMatsA3SS(junctions, strand = "+")
expect_equal(parsed$C1.start, 79679566)
expect_equal(parsed$C1.end, 79679751)
expect_equal(parsed$A1.start, 79685787)
expect_equal(parsed$A2.start, 79685796)
expect_equal(parsed$A2.end, 79685910)
})
test_that("parseMatsA3SS parses an alt. 5' splice site event's junctions", {
junctions <- read.table(
text="102884421 102884501 102884421 102884489 102884812 102885881")
parsed <- parseMatsA5SS(junctions, strand = "+")
expect_equal(parsed$A2.start, 102884421)
expect_equal(parsed$A2.end, 102884489)
expect_equal(parsed$A1.end, 102884501)
expect_equal(parsed$C2.start, 102884812)
expect_equal(parsed$C2.end, 102885881)
})
test_that("parseMatsAFE parses an alt. first exon event's junctions", {
junctions <- read.table(
text = "16308723 16308879 16308967 16309119 16314269 16314426")
parsed <- parseMatsAFE(junctions, strand = "+")
expect_equal(parsed$A2.start, 16308967)
expect_equal(parsed$A2.end, 16309119)
expect_equal(parsed$A1.start, 16308723)
expect_equal(parsed$A1.end, 16308879)
expect_equal(parsed$C2.start, 16314269)
expect_equal(parsed$C2.end, 16314426)
})
test_that("parseMatsALE parses an alt. last exon event's junctions", {
junctions <- read.table(
text = "111858645 111858828 111851063 111851921 111850441 111850543")
parsed <- parseMatsALE(junctions, strand = "+")
expect_equal(parsed$C1.start, 111850441)
expect_equal(parsed$C1.end, 111850543)
expect_equal(parsed$A1.start, 111851063)
expect_equal(parsed$A1.end, 111851921)
expect_equal(parsed$A2.start, 111858645)
expect_equal(parsed$A2.end, 111858828)
})
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