Nothing
tests/testthat/testMisoEvents.R
In psichomics: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
context("Parse MISO splicing events")
library(fastmatch)
test_that("parseMisoAnnotation parses annotation from MISO", {
folder <- "extdata/eventsAnnotSample/miso_annotation"
misoOutput <- system.file(folder, package="psichomics")
miso <- parseMisoAnnotation(misoOutput)
expect_is(miso, "ASevents")
expect_equal(length(miso), 13)
expect_equal(unique(miso$Program), "MISO")
expect_equal(unique(miso$Strand), c("-", "+"))
})
test_that("parseMisoEventID parses an event identifier from MISO", {
eventID <- c("114785@uc001sok.1@uc001soj.1", "114784@uc001bxm.1@uc001bxn.1")
# the annotation is one of the GFF3 files needed to run MISO
gff3 <- system.file("extdata", "miso_AS_annot_example.gff3",
package="psichomics")
annotation <- read.delim(gff3, header=FALSE, comment.char="#")
IDcolumn <- 9
event <- parseMisoEventID(eventID, annotation, IDcolumn)
expect_is(event, "list")
expect_length(event, 2)
expect_is(event[[1]], "data.frame")
expect_equal(unique(event[[1]][[2]]), "AFE")
expect_equivalent(event[[1]][[3]][[1]], "gene")
expect_is(event[[2]], "data.frame")
expect_equal(unique(event[[2]][[2]]), "AFE")
expect_equivalent(event[[2]][[3]][[1]], "gene")
})
test_that("getValidEvents returns valid events depending on the validator", {
event <- read.table(text = "
chr1 SE gene 17233 18061 . - .
chr1 SE jfkdjkf 00000 30000 . - .
chr1 SE mRNA 17233 18061 . - .
chr1 SE exon 17233 17368 . - .
chr1 SE exon 17526 17742 . - .
chr1 SE exon 17915 18061 . - .
chr1 SE mRNA 17233 18061 . - .
chr1 SE exon 17233 17368 . - .
chr1 SE exon 17915 18061 . - .
chr1 SE gene 17233 18061 . - .
chr1 SE mRNA 17233 18061 . - .
chr1 SE exon 17233 17368 . - .
chr1 SE exon 17606 17742 . - .
chr1 SE exon 17915 18061 . - .
chr1 SE mRNA 17233 18061 . - .
chr1 SE exon 17233 17368 . - .
chr1 SE exon 17915 18061 . - .
chr1 SE gene 17915 18061 . - .
chr1 SE gene 17915 18061 . - .
chr1 SE mRNA 17915 18061 . - .
")
validator <- c("gene", "mRNA", rep("exon", 3), "mRNA", rep("exon", 2))
res <- getValidEvents(event, validator)
expect_is(res, "data.frame")
expect_equal(nrow(res), 8)
expect_equal(as.character(res[[3]]), validator)
expect_equal(res, event[10:17, ])
})
test_that("getValidEvents returns one valid event", {
event <- read.table(text = "
chr1 SE gene 17233 18061 . - .
chr1 SE mRNA 17233 18061 . - .
chr1 SE exon 17233 17368 . - .
chr1 SE exon 17606 17742 . - .
chr1 SE exon 17915 18061 . - .
chr1 SE mRNA 17233 18061 . - .
chr1 SE exon 17233 17368 . - .
chr1 SE exon 17915 18061 . - .
")
validator <- c("gene", "mRNA", rep("exon", 3), "mRNA", rep("exon", 2))
res <- getValidEvents(event, validator)
expect_is(res, "data.frame")
expect_equal(nrow(res), 8)
expect_equal(as.character(res[[3]]), validator)
expect_equal(res, event)
})
test_that("getValidEvents returns NULL when there are no valid events", {
event <- read.table(text = "
chr1 SE gene 17233 18061 . - .
chr1 SE dfkdsfjkkfd 00000 30000 . - .
chr1 SE mRNA 17233 18061 . - .
chr1 SE exon 17233 17368 . - .
chr1 SE exon 17526 17742 . - .
chr1 SE exon 17915 18061 . - .
chr1 SE mRNA 17233 18061 . - .
chr1 SE exon 17233 17368 . - .
chr1 SE exon 17915 18061 . - .
chr1 SE gene 17233 18061 . - .
chr1 SE mRNA 17233 18061 . - .
chr1 SE exon 17233 17368 . - .
chr1 SE exon 17606 17742 . - .
chr1 SE ssdfdsfs 110 367 . - .
chr1 SE mRNA 17233 18061 . - .
chr1 SE exon 17233 17368 . - .
chr1 SE exon 17915 18061 . - .
")
validator <- c("gene", "mRNA", rep("exon", 3), "mRNA", rep("exon", 2))
res <- getValidEvents(event, validator)
expect_null(res)
})
# annotation <- read.table(text="
# chr19 AFE gene 50015886 50028830 . + . ID=2217@uc002poi.1@uc002poe.1;Name=2217@uc002poi.1@uc002poe.1;gid=2217@uc002poi.1@uc002poe.1
# chr19 AFE mRNA 50028313 50028830 . + . ID=2217@uc002poi.1@uc002poe.1.A;Parent=2217@uc002poi.1@uc002poe.1;Name=2217@uc002poi.1@uc002poe.1.A;gid=2217@uc002poi.1@uc002poe.1
# chr19 AFE exon 50028313 50028830 . + . ID=2217@uc002poi.1@uc002poe.1.A.0;Parent=2217@uc002poi.1@uc002poe.1.A;Name=2217@uc002poi.1@uc002poe.1.A.0;gid=2217@uc002poi.1@uc002poe.1
# chr19 AFE mRNA 50015886 50016730 . + . ID=2217@uc002poi.1@uc002poe.1.B;Parent=2217@uc002poi.1@uc002poe.1;Name=2217@uc002poi.1@uc002poe.1.B;gid=2217@uc002poi.1@uc002poe.1
# chr19 AFE exon 50015886 50016007 . + . ID=2217@uc002poi.1@uc002poe.1.B.0;Parent=2217@uc002poi.1@uc002poe.1.B;Name=2217@uc002poi.1@uc002poe.1.B.0;gid=2217@uc002poi.1@uc002poe.1
# chr19 AFE exon 50016644 50016730 . + . ID=2217@uc002poi.1@uc002poe.1.B.1;Parent=2217@uc002poi.1@uc002poe.1.B;Name=2217@uc002poi.1@uc002poe.1.B.1;gid=2217@uc002poi.1@uc002poe.1
# chr19 AFE gene 50016492 50017743 . + . ID=2217@uc002poh.1@uc002pog.1;Name=2217@uc002poh.1@uc002pog.1;gid=2217@uc002poh.1@uc002pog.1
# chr19 AFE mRNA 50017468 50017743 . + . ID=2217@uc002poh.1@uc002pog.1.A;Parent=2217@uc002poh.1@uc002pog.1;Name=2217@uc002poh.1@uc002pog.1.A;gid=2217@uc002poh.1@uc002pog.1
# chr19 AFE exon 50017468 50017743 . + . ID=2217@uc002poh.1@uc002pog.1.A.0;Parent=2217@uc002poh.1@uc002pog.1.A;Name=2217@uc002poh.1@uc002pog.1.A.0;gid=2217@uc002poh.1@uc002pog.1
# chr19 AFE mRNA 50016492 50016730 . + . ID=2217@uc002poh.1@uc002pog.1.B;Parent=2217@uc002poh.1@uc002pog.1;Name=2217@uc002poh.1@uc002pog.1.B;gid=2217@uc002poh.1@uc002pog.1
# chr19 AFE exon 50016492 50016730 . + . ID=2217@uc002poh.1@uc002pog.1.B.0;Parent=2217@uc002poh.1@uc002pog.1.B;Name=2217@uc002poh.1@uc002pog.1.B.0;gid=2217@uc002poh.1@uc002pog.1")
#
# event <- c(1, NA, 7)
# next_event <- c(6, NA, NA)
#
# test_that("getDataRows retrieves rows of a data frame", {
# ret <- getDataRows(1, annotation, event, next_event)
# expect_is(ret, "data.frame")
# expect_equal(ret, annotation[1:6, 1:8])
#
# ret <- getDataRows(3, annotation, event, next_event)
# expect_is(ret, "data.frame")
# expect_equal(ret, annotation[7:11, 1:8])
# })
#
# test_that("getDataRows returns NA if value is outside data frame", {
# ret <- getDataRows(2, annotation, event, next_event)
# expect_true(is.na(ret))
# })
#
# test_that("parseMisoID matches events ID (returns NA if not possible)", {
# eventID <- c("2217@uc002poi.1@uc002poe.1", "57705@uc009xob.1@uc001jgy.2",
# "2217@uc002poh.1@uc002pog.1")
# columnID <- 9
#
# events <- parseMisoID(eventID, annotation, columnID)
# expect_equal(length(events), 3)
# expect_equal(events[[1]], annotation[1:6, 1:8])
# expect_true(is.na(events[[2]]))
# expect_equal(events[[3]], annotation[7:11, 1:8])
# })
test_that("parseMisoEvent parses alternative splicing events", {
event <- read.table(text = "
chr1 SE gene 16854 18061 . - .
chr1 SE mRNA 16854 18061 . - .
chr1 SE exon 16854 17055 . - .
chr1 SE exon 17233 17742 . - .
chr1 SE exon 17915 18061 . - .
chr1 SE mRNA 16854 18061 . - .
chr1 SE exon 16854 17955 . - .
chr1 SE exon 17915 18061 . - .")
parsed <- parseMisoEvent(event)
parsed2 <- parseMisoSE(event)
expect_equal(parsed, parsed2)
})
test_that("parseMisoSE parses exon skipping junctions", {
event <- read.table(text = "
chr1 SE gene 1370903 1378262 . + .
chr1 SE mRNA 1370903 1378262 . + .
chr1 SE exon 1370903 1371201 . + .
chr1 SE exon 1372702 1372864 . + .
chr1 SE exon 1374461 1378262 . + .
chr1 SE mRNA 1370903 1378262 . + .
chr1 SE exon 1370903 1371201 . + .
chr1 SE exon 1374461 1378262 . + .
chr1 SE gene 16854 18061 . - .
chr1 SE mRNA 16854 18061 . - .
chr1 SE exon 16854 17055 . - .
chr1 SE exon 17233 17742 . - .
chr1 SE exon 17915 18061 . - .
chr1 SE mRNA 16854 18061 . - .
chr1 SE exon 16854 17955 . - .
chr1 SE exon 17915 18061 . - .")
parsed <- parseMisoSE(event)
expect_equal(parsed$Program, rep("MISO", 2))
expect_equal(parsed$Chromosome, rep("chr1", 2))
expect_equal(parsed$Event.type, rep("SE", 2))
expect_equal(parsed$Strand, c("+", "-"))
# Plus strand
expect_equal(parsed$C1.start[[1]], 1370903)
expect_equal(parsed$C1.end[[1]], 1371201)
expect_equal(parsed$A1.start[[1]], 1372702)
expect_equal(parsed$A1.end[[1]], 1372864)
expect_equal(parsed$C2.start[[1]], 1374461)
expect_equal(parsed$C2.end[[1]], 1378262)
# Minus strand
expect_equal(parsed$C1.start[[2]], 18061)
expect_equal(parsed$C1.end[[2]], 17915)
expect_equal(parsed$A1.start[[2]], 17742)
expect_equal(parsed$A1.end[[2]], 17233)
expect_equal(parsed$C2.start[[2]], 17055)
expect_equal(parsed$C2.end[[2]], 16854)
})
test_that("parseMisoSE doesn't parse unrecognized event", {
event <- read.table(text = "
chr1 SE gene 1370903 1378262 . + .
chr1 SE mRNA 1370903 1378262 . + .
chr1 SE exon 1370903 1371201 . + .
chr1 SE exon 1372702 1372864 . + .
chr1 SE exon 1374461 1378262 . + .
chr7 SE exon 1374461 1378262 . + .
chr1 SE mRNA 1370903 1378262 . + .
chr1 SE exon 1370903 1371201 . + .
chr1 SE exon 1374461 1378262 . + .")
parsed <- parseMisoSE(event)
expect_null(parsed)
})
test_that("parseMisoMXE parses mutually exc. exons junctions", {
event <- read.table(text = "
chr1 MXE gene 764383 788090 . + .
chr1 MXE mRNA 764383 788090 . + .
chr1 MXE exon 764383 764484 . + .
chr1 MXE exon 776580 776753 . + .
chr1 MXE exon 787307 788090 . + .
chr1 MXE mRNA 764383 788090 . + .
chr1 MXE exon 764383 764484 . + .
chr1 MXE exon 783034 783186 . + .
chr1 MXE exon 787307 788090 . + .
chr1 MXE gene 1027371 1051736 . - .
chr1 MXE mRNA 1027371 1051736 . - .
chr1 MXE exon 1027371 1027483 . - .
chr1 MXE exon 1041336 1041429 . - .
chr1 MXE exon 1051440 1051736 . - .
chr1 MXE mRNA 1027371 1051736 . - .
chr1 MXE exon 1027371 1027483 . - .
chr1 MXE exon 1050402 1050455 . - .
chr1 MXE exon 1051440 1051736 . - .")
parsed <- parseMisoMXE(event)
expect_equal(parsed$Program, rep("MISO", 2))
expect_equal(parsed$Chromosome, rep("chr1", 2))
expect_equal(parsed$Event.type, rep("MXE", 2))
expect_equal(parsed$Strand, c("+", "-"))
# Plus strand
expect_equal(parsed$C1.start[[1]], 764383)
expect_equal(parsed$C1.end[[1]], 764484)
expect_equal(parsed$A1.start[[1]], 776580)
expect_equal(parsed$A1.end[[1]], 776753)
expect_equal(parsed$A2.start[[1]], 783034)
expect_equal(parsed$A2.end[[1]], 783186)
expect_equal(parsed$C2.start[[1]], 787307)
expect_equal(parsed$C2.end[[1]], 788090)
# Minus strand
expect_equal(parsed$C1.start[[2]], 1051736)
expect_equal(parsed$C1.end[[2]], 1051440)
expect_equal(parsed$A1.start[[2]], 1041429)
expect_equal(parsed$A1.end[[2]], 1041336)
expect_equal(parsed$A2.start[[2]], 1050455)
expect_equal(parsed$A2.end[[2]], 1050402)
expect_equal(parsed$C2.start[[2]], 1027483)
expect_equal(parsed$C2.end[[2]], 1027371)
})
test_that("parseMisoMXE doesn't parse unrecognized event", {
event <- read.table(text = "
chr1 MXE gene 1027371 1051736 . - .
chr1 MXE mRNA 1027371 1051736 . - .
chr1 MXE exon 1027371 1027483 . - .
chr1 MXE exon 1041336 1041429 . - .
chr1 MXE exon 1051440 1051736 . - .
chr1 MXE mRNA 1027371 1051736 . - .
chr1 MXE exon 1027371 1027483 . - .
chr1 MXE exon 1050402 1050455 . - .
chr6 MXE gene 51440 51736 . + .")
parsed <- parseMisoMXE(event)
expect_null(parsed)
})
test_that("parseMisoRI parses retained intron junctions", {
event <- read.table(text = "
chr1 RI gene 1223053 1223417 . + .
chr1 RI mRNA 1222888 1223216 . + .
chr1 RI exon 1222888 1223216 . + .
chr1 RI mRNA 1222888 1223216 . + .
chr1 RI exon 1222888 1222976 . + .
chr1 RI exon 1223053 1223216 . + .
chr1 RI gene 17233 17742 . - .
chr1 RI mRNA 17233 17742 . - .
chr1 RI exon 17233 17742 . - .
chr1 RI mRNA 17233 17742 . - .
chr1 RI exon 17233 17364 . - .
chr1 RI exon 17601 17742 . - .")
parsed <- parseMisoRI(event)
expect_equal(parsed$Program, rep("MISO", 2))
expect_equal(parsed$Chromosome, rep("chr1", 2))
expect_equal(parsed$Event.type, rep("RI", 2))
expect_equal(parsed$Strand, c("+", "-"))
# Plus strand
expect_equal(parsed$C1.start[[1]], 1222888)
expect_equal(parsed$C1.end[[1]], 1222976)
expect_equal(parsed$C2.start[[1]], 1223053)
expect_equal(parsed$C2.end[[1]], 1223216)
# Minus strand
expect_equal(parsed$C1.start[[2]], 17742)
expect_equal(parsed$C1.end[[2]], 17601)
expect_equal(parsed$C2.start[[2]], 17364)
expect_equal(parsed$C2.end[[2]], 17233)
})
test_that("parseMisoRI doesn't parse unrecognized events", {
event <- read.table(text = "
chr1 RI gene 17233 17742 . - .
chr1 RI mRNA 17233 17742 . - .
chr1 RI exon 17233 17742 . - .
chr10 RI gene 17233 17742 . - .
chr10 RI mRNA 17233 17364 . - .
chr10 RI exon 17601 17742 . - .")
parsed <- parseMisoRI(event)
expect_null(parsed)
})
test_that("parseMisoA5SS parses alt. 5' SS junctions", {
event <- read.table(text = "
chr1 A5SS gene 874655 876686 . + .
chr1 A5SS mRNA 874655 876686 . + .
chr1 A5SS exon 874655 874840 . + .
chr1 A5SS exon 876524 876686 . + .
chr1 A5SS mRNA 874655 876686 . + .
chr1 A5SS exon 874655 874792 . + .
chr1 A5SS exon 876524 876686 . + .
chr1 A5SS gene 17233 17742 . - .
chr1 A5SS mRNA 17233 17742 . - .
chr1 A5SS exon 17233 17368 . - .
chr1 A5SS exon 17526 17742 . - .
chr1 A5SS mRNA 17233 17742 . - .
chr1 A5SS exon 17233 17368 . - .
chr1 A5SS exon 17606 17742 . - .")
parsed <- parseMisoA5SS(event)
expect_equal(parsed$Program, rep("MISO", 2))
expect_equal(parsed$Chromosome, rep("chr1", 2))
expect_equal(parsed$Event.type, rep("A5SS", 2))
expect_equal(parsed$Strand, c("+", "-"))
# Plus strand
expect_equal(parsed$A2.start[[1]], 874655)
expect_equal(parsed$A2.end[[1]], 874792)
expect_equal(parsed$A1.end[[1]], 874840)
expect_equal(parsed$C2.start[[1]], 876524)
expect_equal(parsed$C2.end[[1]], 876686)
# Minus strand
expect_equal(parsed$A2.start[[2]], 17742)
expect_equal(parsed$A2.end[[2]], 17606)
expect_equal(parsed$A1.end[[2]], 17526)
expect_equal(parsed$C2.start[[2]], 17368)
expect_equal(parsed$C2.end[[2]], 17233)
})
test_that("parseMisoA5SS doesn't parse unrecognized events", {
event <- read.table(text = "
chr1 A5SS gene 17233 17742 . - .
chr1 A5SS mRNA 17233 17742 . - .
chr1 A5SS exon 17233 17368 . - .
chr1 A5SS mRNA 17526 17742 . - .
chr1 A5SS mRNA 17233 17742 . - .")
parsed <- parseMisoA5SS(event)
expect_null(parsed)
})
test_that("parseMisoA3SS parses alt. 3' SS junctions", {
event <- read.table(text = "
chr1 A3SS gene 898084 898633 . + .
chr1 A3SS mRNA 898084 898633 . + .
chr1 A3SS exon 898084 898297 . + .
chr1 A3SS exon 898412 898633 . + .
chr1 A3SS mRNA 898084 898633 . + .
chr1 A3SS exon 898084 898297 . + .
chr1 A3SS exon 898489 898633 . + .
chr1 A3SS gene 15796 16765 . - .
chr1 A3SS mRNA 15796 16765 . - .
chr1 A3SS exon 15796 15947 . - .
chr1 A3SS exon 16607 16765 . - .
chr1 A3SS mRNA 15796 16765 . - .
chr1 A3SS exon 15796 15942 . - .
chr1 A3SS exon 16607 16765 . - .")
parsed <- parseMisoA3SS(event)
expect_equal(parsed$Program, rep("MISO", 2))
expect_equal(parsed$Chromosome, rep("chr1", 2))
expect_equal(parsed$Event.type, rep("A3SS", 2))
expect_equal(parsed$Strand, c("+", "-"))
# Plus strand
expect_equal(parsed$C1.start[[1]], 898084)
expect_equal(parsed$C1.end[[1]], 898297)
expect_equal(parsed$A1.start[[1]], 898412)
expect_equal(parsed$A2.start[[1]], 898489)
expect_equal(parsed$A2.end[[1]], 898633)
# Minus strand
expect_equal(parsed$C1.start[[2]], 16765)
expect_equal(parsed$C1.end[[2]], 16607)
expect_equal(parsed$A1.start[[2]], 15947)
expect_equal(parsed$A2.start[[2]], 15942)
expect_equal(parsed$A2.end[[2]], 15796)
})
test_that("parseMisoA3SS doesn't parse unrecognized events", {
event <- read.table(text = "
chr1 A3SS gene 17233 17742 . - .
chr1 A3SS mRNA 17233 17742 . - .
chr1 A3SS exon 17233 17368 . - .
chr1 A3SS mRNA 17526 17742 . - .
chr1 A3SS mRNA 17233 17742 . - .")
parsed <- parseMisoA3SS(event)
expect_null(parsed)
})
test_that("parseMisoTandemUTR parses tandem UTR junctions", {
event <- read.table(text = "
chr12 TandemUTR gene 28702106 28703099 . + .
chr12 TandemUTR mRNA 28702106 28703099 . + .
chr12 TandemUTR exon 28702106 28703099 . + .
chr12 TandemUTR mRNA 28702106 28702181 . + .
chr12 TandemUTR exon 28702106 28702181 . + .
chr19 TandemUTR gene 10663759 10664625 . - .
chr19 TandemUTR mRNA 10663759 10664625 . - .
chr19 TandemUTR exon 10663759 10664625 . - .
chr19 TandemUTR mRNA 10664223 10664625 . - .
chr19 TandemUTR exon 10664223 10664625 . - .")
parsed <- parseMisoTandemUTR(event)
expect_equal(parsed$Program, rep("MISO", 2))
expect_equal(parsed$Chromosome, c("chr12", "chr19"))
expect_equal(parsed$Event.type, rep("TandemUTR", 2))
expect_equal(parsed$Strand, c("+", "-"))
# Plus strand
expect_equal(parsed$A2.start[[1]], 28702106)
expect_equal(parsed$A2.end[[1]], 28703099)
expect_equal(parsed$A1.end[[1]], 28702181)
# Minus strand
expect_equal(parsed$A2.start[[2]], 10664625)
expect_equal(parsed$A2.end[[2]], 10663759)
expect_equal(parsed$A1.end[[2]], 10664223)
})
test_that("parseMisoTandemUTR doesn't parse unrecognized events", {
event <- read.table(text = "
chr1 TandemUTR gene 17233 17742 . - .
chr1 TandemUTR mRNA 17233 17742 . - .
chr1 TandemUTR exon 17233 17368 . - .
chr1 TandemUTR mRNA 17526 17742 . - .")
parsed <- parseMisoTandemUTR(event)
expect_null(parsed)
})
test_that("parseMisoAFE parses alt. first exon junctions", {
# Last exons of each mRNA group
event <- read.table(text = "
chr17 AFE gene 4843303 4848515 . + .
chr17 AFE mRNA 4846721 4848515 . + .
chr17 AFE exon 4846721 4846814 . + .
chr17 AFE exon 4847853 4848515 . + .
chr17 AFE mRNA 4843303 4844288 . + .
chr17 AFE exon 4843303 4843525 . + .
chr17 AFE exon 4843782 4844021 . + .
chr17 AFE exon 4844168 4844288 . + .
chr6 AFE gene 38561740 38607924 . - .
chr6 AFE mRNA 38561740 38563843 . - .
chr6 AFE exon 38561740 38562103 . - .
chr6 AFE exon 38563546 38563843 . - .
chr6 AFE mRNA 38565686 38607924 . - .
chr6 AFE exon 38565686 38565897 . - .
chr6 AFE exon 38607576 38607924 . - .")
parsed <- parseMisoAFE(event)
expect_equal(parsed$Program, rep("MISO", 2))
expect_equal(parsed$Chromosome, c("chr17", "chr6"))
expect_equal(parsed$Event.type, rep("AFE", 2))
expect_equal(parsed$Strand, c("+", "-"))
# Plus strand
expect_equal(parsed$A2.start[[1]], 4844168)
expect_equal(parsed$A2.end[[1]], 4844288)
expect_equal(parsed$A1.start[[1]], 4847853)
expect_equal(parsed$A1.end[[1]], 4848515)
# Minus strand
expect_equal(parsed$A2.start[[2]], 38565897)
expect_equal(parsed$A2.end[[2]], 38565686)
expect_equal(parsed$A1.start[[2]], 38562103)
expect_equal(parsed$A1.end[[2]], 38561740)
})
test_that("parseMisoAFE parses a single alt. first exon event", {
# Last exons of each mRNA group
event <- read.table(text = "
chr17 AFE gene 4843303 4848515 . + .
chr17 AFE mRNA 4846721 4848515 . + .
chr17 AFE exon 4846721 4846814 . + .
chr17 AFE exon 4847853 4848515 . + .
chr17 AFE mRNA 4843303 4844288 . + .
chr17 AFE exon 4843303 4843525 . + .
chr17 AFE exon 4843782 4844021 . + .
chr17 AFE exon 4844168 4844288 . + .")
parsed <- parseMisoAFE(event)
expect_equal(parsed$Program, "MISO")
expect_equal(parsed$Chromosome, "chr17")
expect_equal(parsed$Event.type, "AFE")
expect_equal(parsed$Strand, "+")
expect_equal(parsed$A2.start[[1]], 4844168)
expect_equal(parsed$A2.end[[1]], 4844288)
expect_equal(parsed$A1.start[[1]], 4847853)
expect_equal(parsed$A1.end[[1]], 4848515)
})
test_that("parseMisoAFE doesn't parse unrecognized events", {
event <- read.table(text = "
chr6 AFE gene 30620579 30822593 . - .
chr6 AFE mRNA 30822190 30822593 . - .
chr6 AFE mRNA 30620579 30620982 . - .")
parsed <- parseMisoAFE(event)
expect_null(parsed)
event <- read.table(text = "chr6 AFE gene 30620579 30822593 . - .")
parsed <- parseMisoAFE(event)
expect_null(parsed)
})
test_that("parseMisoALE parses alt. last exon events", {
# First exons of each mRNA group
event <- read.table(text = "
chr19 ALE gene 7830524 7834491 . + .
chr19 ALE mRNA 7830524 7834491 . + .
chr19 ALE exon 7830524 7831693 . + .
chr19 ALE exon 7832402 7832514 . + .
chr19 ALE exon 7833724 7834491 . + .
chr19 ALE mRNA 7833724 7834491 . + .
chr19 ALE exon 7833724 7833929 . + .
chr19 ALE exon 7834259 7834491 . + .
chr17 ALE gene 26931076 26939102 . - .
chr17 ALE mRNA 26931076 26939102 . - .
chr17 ALE exon 26931076 26932233 . - .
chr17 ALE exon 26938786 26938813 . - .
chr17 ALE exon 26939062 26939102 . - .
chr17 ALE mRNA 26934982 26938674 . - .
chr17 ALE exon 26934982 26935547 . - .
chr17 ALE exon 26938562 26938674 . - .")
parsed <- parseMisoALE(event)
expect_equal(parsed$Program, rep("MISO", 2))
expect_equal(parsed$Chromosome, c("chr19", "chr17"))
expect_equal(parsed$Event.type, rep("ALE", 2))
expect_equal(parsed$Strand, c("+", "-"))
# Plus strand
expect_equal(parsed$A1.start[[1]], 7830524)
expect_equal(parsed$A1.end[[1]], 7831693)
expect_equal(parsed$A2.start[[1]], 7833724)
expect_equal(parsed$A2.end[[1]], 7833929)
# Minus strand
expect_equal(parsed$A1.start[[2]], 26939102)
expect_equal(parsed$A1.end[[2]], 26939062)
expect_equal(parsed$A2.start[[2]], 26938674)
expect_equal(parsed$A2.end[[2]], 26938562)
})
test_that("parseMisoALE parses a single alt. last exon event", {
# First exons of each mRNA group
event <- read.table(text = "
chr19 ALE gene 7830524 7834491 . + .
chr19 ALE mRNA 7830524 7834491 . + .
chr19 ALE exon 7830524 7831693 . + .
chr19 ALE exon 7832402 7832514 . + .
chr19 ALE exon 7833724 7834491 . + .
chr19 ALE mRNA 7833724 7834491 . + .
chr19 ALE exon 7833724 7833929 . + .
chr19 ALE exon 7834259 7834491 . + .")
parsed <- parseMisoALE(event)
expect_equal(parsed$Program, "MISO")
expect_equal(parsed$Chromosome, "chr19")
expect_equal(parsed$Event.type, "ALE")
expect_equal(parsed$Strand, "+")
expect_equal(parsed$A1.start[[1]], 7830524)
expect_equal(parsed$A1.end[[1]], 7831693)
expect_equal(parsed$A2.start[[1]], 7833724)
expect_equal(parsed$A2.end[[1]], 7833929)
})
test_that("parseMisoALE doesn't parse unrecognized events", {
event <- read.table(text = "
chr6 ALE gene 30620579 30822593 . - .
chr6 ALE mRNA 30822190 30822593 . - .
chr6 ALE mRNA 30620579 30620982 . - .")
parsed <- parseMisoALE(event)
expect_null(parsed)
event <- read.table(text = "
chr6 ALE gene 30620579 30822593 . - .")
parsed <- parseMisoALE(event)
expect_null(parsed)
})
# test_that("remove_wrong_mRNA removes mRNAs from other chromosomes", {
# event <- read.table(text = "
# chr6 ALE gene 30620579 30822593 . + .
# chr7 ALE mRNA 30620579 30620982 . + .
# chr7 ALE exon 30620579 30620982 . + .
# chr6 ALE mRNA 30822190 30822593 . + .
# chr6 ALE exon 30822190 30822593 . + .")
# new <- remove_wrong_mRNA(event)
# expect_is(new, "data.frame")
# expect_equal(nrow(new), 3)
# expect_equal(new, event[c(1, 4, 5), ])
# })
#
# test_that("remove_wrong_mRNA removes mRNAs outside the event boundary", {
# event <- read.table(text = "
# chr6 ALE gene 30620579 30822593 . + .
# chr6 ALE mRNA 30822190 30822593 . + .
# chr6 ALE exon 30822190 30822593 . + .
# chr6 ALE mRNA 40620579 40620982 . + .
# chr6 ALE exon 40620579 40620982 . + .
# chr6 ALE mRNA 20620579 20620982 . + .
# chr6 ALE exon 20620579 20620982 . + .")
# new <- remove_wrong_mRNA(event)
# expect_is(new, "data.frame")
# expect_equal(nrow(new), 3)
# expect_equal(new, event[1:3, ])
# })
#
# test_that("list_mRNA creates a list with mRNAs and respective exons", {
# event <- read.table(text = "
# chr19 TandemUTR gene 10663759 10664625 . - .
# chr19 TandemUTR mRNA 10663759 10664625 . - .
# chr19 TandemUTR exon 10663759 10664625 . - .
# chr19 TandemUTR mRNA 10664223 10664625 . - .
# chr19 TandemUTR exon 10664223 10664625 . - .
# chr19 TandemUTR mRNA 10664223 10664625 . - .
# chr19 TandemUTR exon 10664223 10664625 . - .
# chr19 TandemUTR mRNA 10664223 10664625 . - .
# chr19 TandemUTR exon 10664223 10664625 . - .")
# mRNA <- list_mRNA(event)
# expect_is(mRNA, "list")
# expect_equal(length(mRNA), 4)
# expect_equal(mRNA[[1]], event[2:3, ])
# expect_equal(mRNA[[2]], event[4:5, ])
# expect_equal(mRNA[[3]], event[6:7, ])
# expect_equal(mRNA[[4]], event[8:9, ])
# })
#
# test_that("remove_duplicated_mRNA removes duplicated mRNAs", {
# event <- read.table(text = "
# chr19 TandemUTR gene 10663759 10664625 . - .
# chr19 TandemUTR mRNA 10663759 10664625 . - .
# chr19 TandemUTR exon 10663759 10664625 . - .
# chr19 TandemUTR mRNA 10664223 10664625 . - .
# chr19 TandemUTR exon 10664223 10664625 . - .
# chr19 TandemUTR mRNA 10664223 10664625 . - .
# chr19 TandemUTR exon 10664223 10664625 . - .
# chr19 TandemUTR mRNA 10664223 10664625 . - .
# chr19 TandemUTR exon 10664223 10664625 . - .")
# mRNA <- list_mRNA(event)
# new <- remove_duplicated_mRNA(mRNA)
# expect_is(new, "list")
# expect_equal(length(new), 2)
# expect_equal(new, mRNA[1:2])
# })
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context("Parse MISO splicing events")
library(fastmatch)
test_that("parseMisoAnnotation parses annotation from MISO", {
folder <- "extdata/eventsAnnotSample/miso_annotation"
misoOutput <- system.file(folder, package="psichomics")
miso <- parseMisoAnnotation(misoOutput)
expect_is(miso, "ASevents")
expect_equal(length(miso), 13)
expect_equal(unique(miso$Program), "MISO")
expect_equal(unique(miso$Strand), c("-", "+"))
})
test_that("parseMisoEventID parses an event identifier from MISO", {
eventID <- c("114785@uc001sok.1@uc001soj.1", "114784@uc001bxm.1@uc001bxn.1")
# the annotation is one of the GFF3 files needed to run MISO
gff3 <- system.file("extdata", "miso_AS_annot_example.gff3",
package="psichomics")
annotation <- read.delim(gff3, header=FALSE, comment.char="#")
IDcolumn <- 9
event <- parseMisoEventID(eventID, annotation, IDcolumn)
expect_is(event, "list")
expect_length(event, 2)
expect_is(event[[1]], "data.frame")
expect_equal(unique(event[[1]][[2]]), "AFE")
expect_equivalent(event[[1]][[3]][[1]], "gene")
expect_is(event[[2]], "data.frame")
expect_equal(unique(event[[2]][[2]]), "AFE")
expect_equivalent(event[[2]][[3]][[1]], "gene")
})
test_that("getValidEvents returns valid events depending on the validator", {
event <- read.table(text = "
chr1 SE gene 17233 18061 . - .
chr1 SE jfkdjkf 00000 30000 . - .
chr1 SE mRNA 17233 18061 . - .
chr1 SE exon 17233 17368 . - .
chr1 SE exon 17526 17742 . - .
chr1 SE exon 17915 18061 . - .
chr1 SE mRNA 17233 18061 . - .
chr1 SE exon 17233 17368 . - .
chr1 SE exon 17915 18061 . - .
chr1 SE gene 17233 18061 . - .
chr1 SE mRNA 17233 18061 . - .
chr1 SE exon 17233 17368 . - .
chr1 SE exon 17606 17742 . - .
chr1 SE exon 17915 18061 . - .
chr1 SE mRNA 17233 18061 . - .
chr1 SE exon 17233 17368 . - .
chr1 SE exon 17915 18061 . - .
chr1 SE gene 17915 18061 . - .
chr1 SE gene 17915 18061 . - .
chr1 SE mRNA 17915 18061 . - .
")
validator <- c("gene", "mRNA", rep("exon", 3), "mRNA", rep("exon", 2))
res <- getValidEvents(event, validator)
expect_is(res, "data.frame")
expect_equal(nrow(res), 8)
expect_equal(as.character(res[[3]]), validator)
expect_equal(res, event[10:17, ])
})
test_that("getValidEvents returns one valid event", {
event <- read.table(text = "
chr1 SE gene 17233 18061 . - .
chr1 SE mRNA 17233 18061 . - .
chr1 SE exon 17233 17368 . - .
chr1 SE exon 17606 17742 . - .
chr1 SE exon 17915 18061 . - .
chr1 SE mRNA 17233 18061 . - .
chr1 SE exon 17233 17368 . - .
chr1 SE exon 17915 18061 . - .
")
validator <- c("gene", "mRNA", rep("exon", 3), "mRNA", rep("exon", 2))
res <- getValidEvents(event, validator)
expect_is(res, "data.frame")
expect_equal(nrow(res), 8)
expect_equal(as.character(res[[3]]), validator)
expect_equal(res, event)
})
test_that("getValidEvents returns NULL when there are no valid events", {
event <- read.table(text = "
chr1 SE gene 17233 18061 . - .
chr1 SE dfkdsfjkkfd 00000 30000 . - .
chr1 SE mRNA 17233 18061 . - .
chr1 SE exon 17233 17368 . - .
chr1 SE exon 17526 17742 . - .
chr1 SE exon 17915 18061 . - .
chr1 SE mRNA 17233 18061 . - .
chr1 SE exon 17233 17368 . - .
chr1 SE exon 17915 18061 . - .
chr1 SE gene 17233 18061 . - .
chr1 SE mRNA 17233 18061 . - .
chr1 SE exon 17233 17368 . - .
chr1 SE exon 17606 17742 . - .
chr1 SE ssdfdsfs 110 367 . - .
chr1 SE mRNA 17233 18061 . - .
chr1 SE exon 17233 17368 . - .
chr1 SE exon 17915 18061 . - .
")
validator <- c("gene", "mRNA", rep("exon", 3), "mRNA", rep("exon", 2))
res <- getValidEvents(event, validator)
expect_null(res)
})
# annotation <- read.table(text="
# chr19 AFE gene 50015886 50028830 . + . ID=2217@uc002poi.1@uc002poe.1;Name=2217@uc002poi.1@uc002poe.1;gid=2217@uc002poi.1@uc002poe.1
# chr19 AFE mRNA 50028313 50028830 . + . ID=2217@uc002poi.1@uc002poe.1.A;Parent=2217@uc002poi.1@uc002poe.1;Name=2217@uc002poi.1@uc002poe.1.A;gid=2217@uc002poi.1@uc002poe.1
# chr19 AFE exon 50028313 50028830 . + . ID=2217@uc002poi.1@uc002poe.1.A.0;Parent=2217@uc002poi.1@uc002poe.1.A;Name=2217@uc002poi.1@uc002poe.1.A.0;gid=2217@uc002poi.1@uc002poe.1
# chr19 AFE mRNA 50015886 50016730 . + . ID=2217@uc002poi.1@uc002poe.1.B;Parent=2217@uc002poi.1@uc002poe.1;Name=2217@uc002poi.1@uc002poe.1.B;gid=2217@uc002poi.1@uc002poe.1
# chr19 AFE exon 50015886 50016007 . + . ID=2217@uc002poi.1@uc002poe.1.B.0;Parent=2217@uc002poi.1@uc002poe.1.B;Name=2217@uc002poi.1@uc002poe.1.B.0;gid=2217@uc002poi.1@uc002poe.1
# chr19 AFE exon 50016644 50016730 . + . ID=2217@uc002poi.1@uc002poe.1.B.1;Parent=2217@uc002poi.1@uc002poe.1.B;Name=2217@uc002poi.1@uc002poe.1.B.1;gid=2217@uc002poi.1@uc002poe.1
# chr19 AFE gene 50016492 50017743 . + . ID=2217@uc002poh.1@uc002pog.1;Name=2217@uc002poh.1@uc002pog.1;gid=2217@uc002poh.1@uc002pog.1
# chr19 AFE mRNA 50017468 50017743 . + . ID=2217@uc002poh.1@uc002pog.1.A;Parent=2217@uc002poh.1@uc002pog.1;Name=2217@uc002poh.1@uc002pog.1.A;gid=2217@uc002poh.1@uc002pog.1
# chr19 AFE exon 50017468 50017743 . + . ID=2217@uc002poh.1@uc002pog.1.A.0;Parent=2217@uc002poh.1@uc002pog.1.A;Name=2217@uc002poh.1@uc002pog.1.A.0;gid=2217@uc002poh.1@uc002pog.1
# chr19 AFE mRNA 50016492 50016730 . + . ID=2217@uc002poh.1@uc002pog.1.B;Parent=2217@uc002poh.1@uc002pog.1;Name=2217@uc002poh.1@uc002pog.1.B;gid=2217@uc002poh.1@uc002pog.1
# chr19 AFE exon 50016492 50016730 . + . ID=2217@uc002poh.1@uc002pog.1.B.0;Parent=2217@uc002poh.1@uc002pog.1.B;Name=2217@uc002poh.1@uc002pog.1.B.0;gid=2217@uc002poh.1@uc002pog.1")
#
# event <- c(1, NA, 7)
# next_event <- c(6, NA, NA)
#
# test_that("getDataRows retrieves rows of a data frame", {
# ret <- getDataRows(1, annotation, event, next_event)
# expect_is(ret, "data.frame")
# expect_equal(ret, annotation[1:6, 1:8])
#
# ret <- getDataRows(3, annotation, event, next_event)
# expect_is(ret, "data.frame")
# expect_equal(ret, annotation[7:11, 1:8])
# })
#
# test_that("getDataRows returns NA if value is outside data frame", {
# ret <- getDataRows(2, annotation, event, next_event)
# expect_true(is.na(ret))
# })
#
# test_that("parseMisoID matches events ID (returns NA if not possible)", {
# eventID <- c("2217@uc002poi.1@uc002poe.1", "57705@uc009xob.1@uc001jgy.2",
# "2217@uc002poh.1@uc002pog.1")
# columnID <- 9
#
# events <- parseMisoID(eventID, annotation, columnID)
# expect_equal(length(events), 3)
# expect_equal(events[[1]], annotation[1:6, 1:8])
# expect_true(is.na(events[[2]]))
# expect_equal(events[[3]], annotation[7:11, 1:8])
# })
test_that("parseMisoEvent parses alternative splicing events", {
event <- read.table(text = "
chr1 SE gene 16854 18061 . - .
chr1 SE mRNA 16854 18061 . - .
chr1 SE exon 16854 17055 . - .
chr1 SE exon 17233 17742 . - .
chr1 SE exon 17915 18061 . - .
chr1 SE mRNA 16854 18061 . - .
chr1 SE exon 16854 17955 . - .
chr1 SE exon 17915 18061 . - .")
parsed <- parseMisoEvent(event)
parsed2 <- parseMisoSE(event)
expect_equal(parsed, parsed2)
})
test_that("parseMisoSE parses exon skipping junctions", {
event <- read.table(text = "
chr1 SE gene 1370903 1378262 . + .
chr1 SE mRNA 1370903 1378262 . + .
chr1 SE exon 1370903 1371201 . + .
chr1 SE exon 1372702 1372864 . + .
chr1 SE exon 1374461 1378262 . + .
chr1 SE mRNA 1370903 1378262 . + .
chr1 SE exon 1370903 1371201 . + .
chr1 SE exon 1374461 1378262 . + .
chr1 SE gene 16854 18061 . - .
chr1 SE mRNA 16854 18061 . - .
chr1 SE exon 16854 17055 . - .
chr1 SE exon 17233 17742 . - .
chr1 SE exon 17915 18061 . - .
chr1 SE mRNA 16854 18061 . - .
chr1 SE exon 16854 17955 . - .
chr1 SE exon 17915 18061 . - .")
parsed <- parseMisoSE(event)
expect_equal(parsed$Program, rep("MISO", 2))
expect_equal(parsed$Chromosome, rep("chr1", 2))
expect_equal(parsed$Event.type, rep("SE", 2))
expect_equal(parsed$Strand, c("+", "-"))
# Plus strand
expect_equal(parsed$C1.start[[1]], 1370903)
expect_equal(parsed$C1.end[[1]], 1371201)
expect_equal(parsed$A1.start[[1]], 1372702)
expect_equal(parsed$A1.end[[1]], 1372864)
expect_equal(parsed$C2.start[[1]], 1374461)
expect_equal(parsed$C2.end[[1]], 1378262)
# Minus strand
expect_equal(parsed$C1.start[[2]], 18061)
expect_equal(parsed$C1.end[[2]], 17915)
expect_equal(parsed$A1.start[[2]], 17742)
expect_equal(parsed$A1.end[[2]], 17233)
expect_equal(parsed$C2.start[[2]], 17055)
expect_equal(parsed$C2.end[[2]], 16854)
})
test_that("parseMisoSE doesn't parse unrecognized event", {
event <- read.table(text = "
chr1 SE gene 1370903 1378262 . + .
chr1 SE mRNA 1370903 1378262 . + .
chr1 SE exon 1370903 1371201 . + .
chr1 SE exon 1372702 1372864 . + .
chr1 SE exon 1374461 1378262 . + .
chr7 SE exon 1374461 1378262 . + .
chr1 SE mRNA 1370903 1378262 . + .
chr1 SE exon 1370903 1371201 . + .
chr1 SE exon 1374461 1378262 . + .")
parsed <- parseMisoSE(event)
expect_null(parsed)
})
test_that("parseMisoMXE parses mutually exc. exons junctions", {
event <- read.table(text = "
chr1 MXE gene 764383 788090 . + .
chr1 MXE mRNA 764383 788090 . + .
chr1 MXE exon 764383 764484 . + .
chr1 MXE exon 776580 776753 . + .
chr1 MXE exon 787307 788090 . + .
chr1 MXE mRNA 764383 788090 . + .
chr1 MXE exon 764383 764484 . + .
chr1 MXE exon 783034 783186 . + .
chr1 MXE exon 787307 788090 . + .
chr1 MXE gene 1027371 1051736 . - .
chr1 MXE mRNA 1027371 1051736 . - .
chr1 MXE exon 1027371 1027483 . - .
chr1 MXE exon 1041336 1041429 . - .
chr1 MXE exon 1051440 1051736 . - .
chr1 MXE mRNA 1027371 1051736 . - .
chr1 MXE exon 1027371 1027483 . - .
chr1 MXE exon 1050402 1050455 . - .
chr1 MXE exon 1051440 1051736 . - .")
parsed <- parseMisoMXE(event)
expect_equal(parsed$Program, rep("MISO", 2))
expect_equal(parsed$Chromosome, rep("chr1", 2))
expect_equal(parsed$Event.type, rep("MXE", 2))
expect_equal(parsed$Strand, c("+", "-"))
# Plus strand
expect_equal(parsed$C1.start[[1]], 764383)
expect_equal(parsed$C1.end[[1]], 764484)
expect_equal(parsed$A1.start[[1]], 776580)
expect_equal(parsed$A1.end[[1]], 776753)
expect_equal(parsed$A2.start[[1]], 783034)
expect_equal(parsed$A2.end[[1]], 783186)
expect_equal(parsed$C2.start[[1]], 787307)
expect_equal(parsed$C2.end[[1]], 788090)
# Minus strand
expect_equal(parsed$C1.start[[2]], 1051736)
expect_equal(parsed$C1.end[[2]], 1051440)
expect_equal(parsed$A1.start[[2]], 1041429)
expect_equal(parsed$A1.end[[2]], 1041336)
expect_equal(parsed$A2.start[[2]], 1050455)
expect_equal(parsed$A2.end[[2]], 1050402)
expect_equal(parsed$C2.start[[2]], 1027483)
expect_equal(parsed$C2.end[[2]], 1027371)
})
test_that("parseMisoMXE doesn't parse unrecognized event", {
event <- read.table(text = "
chr1 MXE gene 1027371 1051736 . - .
chr1 MXE mRNA 1027371 1051736 . - .
chr1 MXE exon 1027371 1027483 . - .
chr1 MXE exon 1041336 1041429 . - .
chr1 MXE exon 1051440 1051736 . - .
chr1 MXE mRNA 1027371 1051736 . - .
chr1 MXE exon 1027371 1027483 . - .
chr1 MXE exon 1050402 1050455 . - .
chr6 MXE gene 51440 51736 . + .")
parsed <- parseMisoMXE(event)
expect_null(parsed)
})
test_that("parseMisoRI parses retained intron junctions", {
event <- read.table(text = "
chr1 RI gene 1223053 1223417 . + .
chr1 RI mRNA 1222888 1223216 . + .
chr1 RI exon 1222888 1223216 . + .
chr1 RI mRNA 1222888 1223216 . + .
chr1 RI exon 1222888 1222976 . + .
chr1 RI exon 1223053 1223216 . + .
chr1 RI gene 17233 17742 . - .
chr1 RI mRNA 17233 17742 . - .
chr1 RI exon 17233 17742 . - .
chr1 RI mRNA 17233 17742 . - .
chr1 RI exon 17233 17364 . - .
chr1 RI exon 17601 17742 . - .")
parsed <- parseMisoRI(event)
expect_equal(parsed$Program, rep("MISO", 2))
expect_equal(parsed$Chromosome, rep("chr1", 2))
expect_equal(parsed$Event.type, rep("RI", 2))
expect_equal(parsed$Strand, c("+", "-"))
# Plus strand
expect_equal(parsed$C1.start[[1]], 1222888)
expect_equal(parsed$C1.end[[1]], 1222976)
expect_equal(parsed$C2.start[[1]], 1223053)
expect_equal(parsed$C2.end[[1]], 1223216)
# Minus strand
expect_equal(parsed$C1.start[[2]], 17742)
expect_equal(parsed$C1.end[[2]], 17601)
expect_equal(parsed$C2.start[[2]], 17364)
expect_equal(parsed$C2.end[[2]], 17233)
})
test_that("parseMisoRI doesn't parse unrecognized events", {
event <- read.table(text = "
chr1 RI gene 17233 17742 . - .
chr1 RI mRNA 17233 17742 . - .
chr1 RI exon 17233 17742 . - .
chr10 RI gene 17233 17742 . - .
chr10 RI mRNA 17233 17364 . - .
chr10 RI exon 17601 17742 . - .")
parsed <- parseMisoRI(event)
expect_null(parsed)
})
test_that("parseMisoA5SS parses alt. 5' SS junctions", {
event <- read.table(text = "
chr1 A5SS gene 874655 876686 . + .
chr1 A5SS mRNA 874655 876686 . + .
chr1 A5SS exon 874655 874840 . + .
chr1 A5SS exon 876524 876686 . + .
chr1 A5SS mRNA 874655 876686 . + .
chr1 A5SS exon 874655 874792 . + .
chr1 A5SS exon 876524 876686 . + .
chr1 A5SS gene 17233 17742 . - .
chr1 A5SS mRNA 17233 17742 . - .
chr1 A5SS exon 17233 17368 . - .
chr1 A5SS exon 17526 17742 . - .
chr1 A5SS mRNA 17233 17742 . - .
chr1 A5SS exon 17233 17368 . - .
chr1 A5SS exon 17606 17742 . - .")
parsed <- parseMisoA5SS(event)
expect_equal(parsed$Program, rep("MISO", 2))
expect_equal(parsed$Chromosome, rep("chr1", 2))
expect_equal(parsed$Event.type, rep("A5SS", 2))
expect_equal(parsed$Strand, c("+", "-"))
# Plus strand
expect_equal(parsed$A2.start[[1]], 874655)
expect_equal(parsed$A2.end[[1]], 874792)
expect_equal(parsed$A1.end[[1]], 874840)
expect_equal(parsed$C2.start[[1]], 876524)
expect_equal(parsed$C2.end[[1]], 876686)
# Minus strand
expect_equal(parsed$A2.start[[2]], 17742)
expect_equal(parsed$A2.end[[2]], 17606)
expect_equal(parsed$A1.end[[2]], 17526)
expect_equal(parsed$C2.start[[2]], 17368)
expect_equal(parsed$C2.end[[2]], 17233)
})
test_that("parseMisoA5SS doesn't parse unrecognized events", {
event <- read.table(text = "
chr1 A5SS gene 17233 17742 . - .
chr1 A5SS mRNA 17233 17742 . - .
chr1 A5SS exon 17233 17368 . - .
chr1 A5SS mRNA 17526 17742 . - .
chr1 A5SS mRNA 17233 17742 . - .")
parsed <- parseMisoA5SS(event)
expect_null(parsed)
})
test_that("parseMisoA3SS parses alt. 3' SS junctions", {
event <- read.table(text = "
chr1 A3SS gene 898084 898633 . + .
chr1 A3SS mRNA 898084 898633 . + .
chr1 A3SS exon 898084 898297 . + .
chr1 A3SS exon 898412 898633 . + .
chr1 A3SS mRNA 898084 898633 . + .
chr1 A3SS exon 898084 898297 . + .
chr1 A3SS exon 898489 898633 . + .
chr1 A3SS gene 15796 16765 . - .
chr1 A3SS mRNA 15796 16765 . - .
chr1 A3SS exon 15796 15947 . - .
chr1 A3SS exon 16607 16765 . - .
chr1 A3SS mRNA 15796 16765 . - .
chr1 A3SS exon 15796 15942 . - .
chr1 A3SS exon 16607 16765 . - .")
parsed <- parseMisoA3SS(event)
expect_equal(parsed$Program, rep("MISO", 2))
expect_equal(parsed$Chromosome, rep("chr1", 2))
expect_equal(parsed$Event.type, rep("A3SS", 2))
expect_equal(parsed$Strand, c("+", "-"))
# Plus strand
expect_equal(parsed$C1.start[[1]], 898084)
expect_equal(parsed$C1.end[[1]], 898297)
expect_equal(parsed$A1.start[[1]], 898412)
expect_equal(parsed$A2.start[[1]], 898489)
expect_equal(parsed$A2.end[[1]], 898633)
# Minus strand
expect_equal(parsed$C1.start[[2]], 16765)
expect_equal(parsed$C1.end[[2]], 16607)
expect_equal(parsed$A1.start[[2]], 15947)
expect_equal(parsed$A2.start[[2]], 15942)
expect_equal(parsed$A2.end[[2]], 15796)
})
test_that("parseMisoA3SS doesn't parse unrecognized events", {
event <- read.table(text = "
chr1 A3SS gene 17233 17742 . - .
chr1 A3SS mRNA 17233 17742 . - .
chr1 A3SS exon 17233 17368 . - .
chr1 A3SS mRNA 17526 17742 . - .
chr1 A3SS mRNA 17233 17742 . - .")
parsed <- parseMisoA3SS(event)
expect_null(parsed)
})
test_that("parseMisoTandemUTR parses tandem UTR junctions", {
event <- read.table(text = "
chr12 TandemUTR gene 28702106 28703099 . + .
chr12 TandemUTR mRNA 28702106 28703099 . + .
chr12 TandemUTR exon 28702106 28703099 . + .
chr12 TandemUTR mRNA 28702106 28702181 . + .
chr12 TandemUTR exon 28702106 28702181 . + .
chr19 TandemUTR gene 10663759 10664625 . - .
chr19 TandemUTR mRNA 10663759 10664625 . - .
chr19 TandemUTR exon 10663759 10664625 . - .
chr19 TandemUTR mRNA 10664223 10664625 . - .
chr19 TandemUTR exon 10664223 10664625 . - .")
parsed <- parseMisoTandemUTR(event)
expect_equal(parsed$Program, rep("MISO", 2))
expect_equal(parsed$Chromosome, c("chr12", "chr19"))
expect_equal(parsed$Event.type, rep("TandemUTR", 2))
expect_equal(parsed$Strand, c("+", "-"))
# Plus strand
expect_equal(parsed$A2.start[[1]], 28702106)
expect_equal(parsed$A2.end[[1]], 28703099)
expect_equal(parsed$A1.end[[1]], 28702181)
# Minus strand
expect_equal(parsed$A2.start[[2]], 10664625)
expect_equal(parsed$A2.end[[2]], 10663759)
expect_equal(parsed$A1.end[[2]], 10664223)
})
test_that("parseMisoTandemUTR doesn't parse unrecognized events", {
event <- read.table(text = "
chr1 TandemUTR gene 17233 17742 . - .
chr1 TandemUTR mRNA 17233 17742 . - .
chr1 TandemUTR exon 17233 17368 . - .
chr1 TandemUTR mRNA 17526 17742 . - .")
parsed <- parseMisoTandemUTR(event)
expect_null(parsed)
})
test_that("parseMisoAFE parses alt. first exon junctions", {
# Last exons of each mRNA group
event <- read.table(text = "
chr17 AFE gene 4843303 4848515 . + .
chr17 AFE mRNA 4846721 4848515 . + .
chr17 AFE exon 4846721 4846814 . + .
chr17 AFE exon 4847853 4848515 . + .
chr17 AFE mRNA 4843303 4844288 . + .
chr17 AFE exon 4843303 4843525 . + .
chr17 AFE exon 4843782 4844021 . + .
chr17 AFE exon 4844168 4844288 . + .
chr6 AFE gene 38561740 38607924 . - .
chr6 AFE mRNA 38561740 38563843 . - .
chr6 AFE exon 38561740 38562103 . - .
chr6 AFE exon 38563546 38563843 . - .
chr6 AFE mRNA 38565686 38607924 . - .
chr6 AFE exon 38565686 38565897 . - .
chr6 AFE exon 38607576 38607924 . - .")
parsed <- parseMisoAFE(event)
expect_equal(parsed$Program, rep("MISO", 2))
expect_equal(parsed$Chromosome, c("chr17", "chr6"))
expect_equal(parsed$Event.type, rep("AFE", 2))
expect_equal(parsed$Strand, c("+", "-"))
# Plus strand
expect_equal(parsed$A2.start[[1]], 4844168)
expect_equal(parsed$A2.end[[1]], 4844288)
expect_equal(parsed$A1.start[[1]], 4847853)
expect_equal(parsed$A1.end[[1]], 4848515)
# Minus strand
expect_equal(parsed$A2.start[[2]], 38565897)
expect_equal(parsed$A2.end[[2]], 38565686)
expect_equal(parsed$A1.start[[2]], 38562103)
expect_equal(parsed$A1.end[[2]], 38561740)
})
test_that("parseMisoAFE parses a single alt. first exon event", {
# Last exons of each mRNA group
event <- read.table(text = "
chr17 AFE gene 4843303 4848515 . + .
chr17 AFE mRNA 4846721 4848515 . + .
chr17 AFE exon 4846721 4846814 . + .
chr17 AFE exon 4847853 4848515 . + .
chr17 AFE mRNA 4843303 4844288 . + .
chr17 AFE exon 4843303 4843525 . + .
chr17 AFE exon 4843782 4844021 . + .
chr17 AFE exon 4844168 4844288 . + .")
parsed <- parseMisoAFE(event)
expect_equal(parsed$Program, "MISO")
expect_equal(parsed$Chromosome, "chr17")
expect_equal(parsed$Event.type, "AFE")
expect_equal(parsed$Strand, "+")
expect_equal(parsed$A2.start[[1]], 4844168)
expect_equal(parsed$A2.end[[1]], 4844288)
expect_equal(parsed$A1.start[[1]], 4847853)
expect_equal(parsed$A1.end[[1]], 4848515)
})
test_that("parseMisoAFE doesn't parse unrecognized events", {
event <- read.table(text = "
chr6 AFE gene 30620579 30822593 . - .
chr6 AFE mRNA 30822190 30822593 . - .
chr6 AFE mRNA 30620579 30620982 . - .")
parsed <- parseMisoAFE(event)
expect_null(parsed)
event <- read.table(text = "chr6 AFE gene 30620579 30822593 . - .")
parsed <- parseMisoAFE(event)
expect_null(parsed)
})
test_that("parseMisoALE parses alt. last exon events", {
# First exons of each mRNA group
event <- read.table(text = "
chr19 ALE gene 7830524 7834491 . + .
chr19 ALE mRNA 7830524 7834491 . + .
chr19 ALE exon 7830524 7831693 . + .
chr19 ALE exon 7832402 7832514 . + .
chr19 ALE exon 7833724 7834491 . + .
chr19 ALE mRNA 7833724 7834491 . + .
chr19 ALE exon 7833724 7833929 . + .
chr19 ALE exon 7834259 7834491 . + .
chr17 ALE gene 26931076 26939102 . - .
chr17 ALE mRNA 26931076 26939102 . - .
chr17 ALE exon 26931076 26932233 . - .
chr17 ALE exon 26938786 26938813 . - .
chr17 ALE exon 26939062 26939102 . - .
chr17 ALE mRNA 26934982 26938674 . - .
chr17 ALE exon 26934982 26935547 . - .
chr17 ALE exon 26938562 26938674 . - .")
parsed <- parseMisoALE(event)
expect_equal(parsed$Program, rep("MISO", 2))
expect_equal(parsed$Chromosome, c("chr19", "chr17"))
expect_equal(parsed$Event.type, rep("ALE", 2))
expect_equal(parsed$Strand, c("+", "-"))
# Plus strand
expect_equal(parsed$A1.start[[1]], 7830524)
expect_equal(parsed$A1.end[[1]], 7831693)
expect_equal(parsed$A2.start[[1]], 7833724)
expect_equal(parsed$A2.end[[1]], 7833929)
# Minus strand
expect_equal(parsed$A1.start[[2]], 26939102)
expect_equal(parsed$A1.end[[2]], 26939062)
expect_equal(parsed$A2.start[[2]], 26938674)
expect_equal(parsed$A2.end[[2]], 26938562)
})
test_that("parseMisoALE parses a single alt. last exon event", {
# First exons of each mRNA group
event <- read.table(text = "
chr19 ALE gene 7830524 7834491 . + .
chr19 ALE mRNA 7830524 7834491 . + .
chr19 ALE exon 7830524 7831693 . + .
chr19 ALE exon 7832402 7832514 . + .
chr19 ALE exon 7833724 7834491 . + .
chr19 ALE mRNA 7833724 7834491 . + .
chr19 ALE exon 7833724 7833929 . + .
chr19 ALE exon 7834259 7834491 . + .")
parsed <- parseMisoALE(event)
expect_equal(parsed$Program, "MISO")
expect_equal(parsed$Chromosome, "chr19")
expect_equal(parsed$Event.type, "ALE")
expect_equal(parsed$Strand, "+")
expect_equal(parsed$A1.start[[1]], 7830524)
expect_equal(parsed$A1.end[[1]], 7831693)
expect_equal(parsed$A2.start[[1]], 7833724)
expect_equal(parsed$A2.end[[1]], 7833929)
})
test_that("parseMisoALE doesn't parse unrecognized events", {
event <- read.table(text = "
chr6 ALE gene 30620579 30822593 . - .
chr6 ALE mRNA 30822190 30822593 . - .
chr6 ALE mRNA 30620579 30620982 . - .")
parsed <- parseMisoALE(event)
expect_null(parsed)
event <- read.table(text = "
chr6 ALE gene 30620579 30822593 . - .")
parsed <- parseMisoALE(event)
expect_null(parsed)
})
# test_that("remove_wrong_mRNA removes mRNAs from other chromosomes", {
# event <- read.table(text = "
# chr6 ALE gene 30620579 30822593 . + .
# chr7 ALE mRNA 30620579 30620982 . + .
# chr7 ALE exon 30620579 30620982 . + .
# chr6 ALE mRNA 30822190 30822593 . + .
# chr6 ALE exon 30822190 30822593 . + .")
# new <- remove_wrong_mRNA(event)
# expect_is(new, "data.frame")
# expect_equal(nrow(new), 3)
# expect_equal(new, event[c(1, 4, 5), ])
# })
#
# test_that("remove_wrong_mRNA removes mRNAs outside the event boundary", {
# event <- read.table(text = "
# chr6 ALE gene 30620579 30822593 . + .
# chr6 ALE mRNA 30822190 30822593 . + .
# chr6 ALE exon 30822190 30822593 . + .
# chr6 ALE mRNA 40620579 40620982 . + .
# chr6 ALE exon 40620579 40620982 . + .
# chr6 ALE mRNA 20620579 20620982 . + .
# chr6 ALE exon 20620579 20620982 . + .")
# new <- remove_wrong_mRNA(event)
# expect_is(new, "data.frame")
# expect_equal(nrow(new), 3)
# expect_equal(new, event[1:3, ])
# })
#
# test_that("list_mRNA creates a list with mRNAs and respective exons", {
# event <- read.table(text = "
# chr19 TandemUTR gene 10663759 10664625 . - .
# chr19 TandemUTR mRNA 10663759 10664625 . - .
# chr19 TandemUTR exon 10663759 10664625 . - .
# chr19 TandemUTR mRNA 10664223 10664625 . - .
# chr19 TandemUTR exon 10664223 10664625 . - .
# chr19 TandemUTR mRNA 10664223 10664625 . - .
# chr19 TandemUTR exon 10664223 10664625 . - .
# chr19 TandemUTR mRNA 10664223 10664625 . - .
# chr19 TandemUTR exon 10664223 10664625 . - .")
# mRNA <- list_mRNA(event)
# expect_is(mRNA, "list")
# expect_equal(length(mRNA), 4)
# expect_equal(mRNA[[1]], event[2:3, ])
# expect_equal(mRNA[[2]], event[4:5, ])
# expect_equal(mRNA[[3]], event[6:7, ])
# expect_equal(mRNA[[4]], event[8:9, ])
# })
#
# test_that("remove_duplicated_mRNA removes duplicated mRNAs", {
# event <- read.table(text = "
# chr19 TandemUTR gene 10663759 10664625 . - .
# chr19 TandemUTR mRNA 10663759 10664625 . - .
# chr19 TandemUTR exon 10663759 10664625 . - .
# chr19 TandemUTR mRNA 10664223 10664625 . - .
# chr19 TandemUTR exon 10664223 10664625 . - .
# chr19 TandemUTR mRNA 10664223 10664625 . - .
# chr19 TandemUTR exon 10664223 10664625 . - .
# chr19 TandemUTR mRNA 10664223 10664625 . - .
# chr19 TandemUTR exon 10664223 10664625 . - .")
# mRNA <- list_mRNA(event)
# new <- remove_duplicated_mRNA(mRNA)
# expect_is(new, "list")
# expect_equal(length(new), 2)
# expect_equal(new, mRNA[1:2])
# })
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