tests/testthat/test_gChain.R
In mskilab/gChain: R Package Providing Additional Capabilities and Speed for GenomicRanges Operations
library(gChain)
library(testthat)
library(gUtils)
library(gTrack)
Sys.setenv(DEFAULT_BSGENOME = "BSgenome.Hsapiens.UCSC.hg19::Hsapiens")
gr = GRanges(1, IRanges(c(3,7,13), c(5,9,16)), strand=c('+','-','-'), seqinfo=Seqinfo("1", 25), name=c("A","B","C"))
gr2 = GRanges(1, IRanges(c(1,9), c(6,14)), strand=c('+','-'), seqinfo=Seqinfo("1", 25), field=c(1,2))
dt = data.table(seqnames=1, start=c(2,5,10), end=c(3,8,15))
i1 = IRanges(c(3,7,13), c(5,9,16))
i2 = IRanges(c(1,9, 32), c(6,14, 45))
test_that('testing gChain() works', {
expect_true(is(gChain(), 'gChain'))
expect_equal(length(gChain()), 1)
expect_equal(width(gChain()$x), 0)
### dim()
expect_equal(dim(gChain())[1], 0)
expect_equal(dim(gChain())[2], 0)
### links()
expect_equal(width(links(gChain())$x), 0)
expect_equal(width(links(gChain())$y), 0)
### values()
expect_equal(values(gChain()), data.frame())
## c()
expect_equal(values(c(gChain(gr), gChain(gr2))), data.frame())
expect_equal(values(gChain(x = si, y = si)), data.frame())
expect_equal(values(gChain(x = GRanges(), y = NULL)), data.frame())
expect_equal(values(gChain(x = NULL, y = GRanges())), data.frame())
expect_equal(values(c(gChain())), data.frame())
## Error: At least one of the objects to be concatanted is not a gChain
expect_error(c(gChain(gr), c('foo')))
## check 'show()' works
expect_error(show(gChain()), NA)
## if (length(x)>0 & length(y)>0 & length(x) != length(y)){
expect_error(gChain(gr, gr2))
## if (is(x, 'IRanges')){
expect_equal(dim(gChain(x = i1))[1], 16)
expect_equal(dim(gChain(x = i1))[2], 16)
## if (is(y, 'IRanges')){
expect_equal(dim(gChain(y = i2))[1], 45)
expect_equal(dim(gChain(y = i2))[2], 45)
## Error in validObject(.Object) :
## invalid class “gChain” object: 1: All intervals pairs must have a single scale
## invalid class “gChain” object: 2: Scales not consistent with interval pair widths and .pad.left / .pad.right properties.
expect_error(gChain(i2, i1))
## if (!is(x, 'GRanges') | !is(y, 'GRanges')){
## Error: inputs to gChain() must be of the type GRanges
expect_error(gChain(grl2))
expect_equal(dim(gChain(gr[1:2], gr2, val = 42))[1], 25)
## if (ncol(val)>0 & nrow(val)==1){
expect_equal(dim(gChain(gr[1:2], gr2, val = data.frame(c(42))))[1], 25)
## if (is.vector(val)){
expect_equal(dim(gChain(gr[1:2], gr2, val = c(42, 13)))[1], 25)
## x = NULL, y = NULL, pad.left = 0, pad.right = 0, scale = NULL, val = data.frame())
## if (is.null(scale)){
expect_equal(dim((gChain(gr2, scale=1)))[1], 25)
## what does scale < 0 mean?
expect_equal(dim((gChain(gr2, scale=-1)))[1], 25)
})
test_that('testing gMultiply() works', {
gc1 = gChain(gr, gr)
gc2 = gChain(gr, gr)
gc2 = gMultiply(gc1, gc2)
## expect_equal(gc1, gc2)
expect_equal(gMultiply(gc1, gc2), gMultiply(gc2, gc1))
## empty GRanges()
foo1 = gChain(grl.unlist(grl1), grl.unlist(grl2)[1:500])
foo2 = gChain(example_dnase[1:200])
multiplied = gMultiply(foo1, foo2)
expect_equal(multiplied, GRanges())
})
test_that('testing scale() works', {
expect_equal(scale(gChain()), 1)
})
test_that('testing lift() works', {
expect_equal(length(gChain()), 1)
foo = gChain(grl.unlist(grl2))
expect_equal(length(lift(foo, grl.unlist(grl2))), 502)
expect_equal(length(lift(foo, grl.unlist(grl2), split.grl = TRUE)), 502)
## if (!(format %in% c('GRanges', 'df', 'df.all', 'matrix', 'GRangesList', 'gTrack'))){
expect_error(length(lift(foo, grl.unlist(grl2), format='foobar')))
expect_error(lift(foo, c(1))) ## Error in .local(.Object, x, ...) : Error: x must be Granges object
expect_equal(length(lift(foo, grl2)), 251)
expect_equal(length(lift(foo, IRanges(c(3,7,13), c(5,9,16)))), 0)
## data.frame
expect_true(is(lift(foo, grl.unlist(grl2), format='df'), 'data.frame'))
expect_equal(dim(lift(foo, grl.unlist(grl2), format='df'))[1], 502)
expect_equal(dim(lift(foo, grl.unlist(grl2), format='df'))[2], 4)
## GRanges
expect_equal(length(lift(foo, grl.unlist(grl2), format='GRanges')), 502)
expect_true(is(lift(foo, grl.unlist(grl2), format='GRanges'), 'GRanges'))
## gTrack
expect_equal(dim(lift(foo, grl.unlist(grl2), format='gTrack'))[1], 502)
expect_equal(dim(lift(foo, grl.unlist(grl2), format='gTrack'))[2], 4)
## matrix
expect_equal(dim(lift(foo, grl.unlist(grl2), format='matrix'))[1], 502)
expect_equal(dim(lift(foo, grl.unlist(grl2), format='matrix'))[2], 4)
##
expect_true(is(lift(gChain(example_genes), gTrack(example_genes), format='gTrack'), 'gTrack'))
## if (is(x, 'gTrack')){
## if (length(x)>1){
expect_true(is(lift(gChain(example_genes), c(gTrack(example_genes), gTrack(example_dnase), gTrack(grl.unlist(grl2))), format='gTrack'), 'gTrack'))
})
test_that('testing scale()) works', {
expect_equal(scale(gChain()), 1)
})
test_that('testing pads() works', {
expect_equal(pads(gChain())$pad.left, 0)
expect_equal(pads(gChain())$pad.right, 0)
})
test_that('testing genomes() works', {
expect_equal(width(genomes(gChain())$x), 0)
expect_equal(width(genomes(gChain())$y), 0)
})
test_that('testing "*" works', {
## identity multiplication
## setMethod("*", signature(e1 = "gChain", e2 = "GRanges"), function(e1, e2)
gc1 = gChain(gr,gr)
gc2 = gChain(gr,gr)
## gc2 = gc1 * gc2
## expect_equal(gc1, gc2)
expect_equal((gc1 * gc2), (gc2 * gc1))
## with GRList
## setMethod("*", signature(e1 = "gChain", e2 = "GRangesList"), function(e1, e2)
expect_equal(length(gc1 * grl2), 0)
## with GRanges
expect_equal(length(gc1 * gr2), 3)
})
test_that('testing expand() works', {
### setMethod("expand", signature(x = "gChain"), function(x, space = NULL, shift.x = FALSE, shift.y = TRUE)
expect_true(is(expand(gChain(grl.unlist(grl2))), 'gChain'))
expect_equal(dim(expand(gChain(grl.unlist(grl2))))[1], 3095693983)
expect_equal(dim(expand(gChain(grl.unlist(grl2))))[2], 3095693983)
##
expect_equal(dim(expand(gChain(grl.unlist(grl2)[1:25], grl.unlist(grl1)[1:25])))[1], 3095693983)
expect_equal(dim(expand(gChain(grl.unlist(grl2)[1:25], grl.unlist(grl1)[1:25])))[2], 3095693983)
expect_equal(dim(expand(gChain(grl.unlist(grl2)[1:500], grl.unlist(grl1))))[1], 3095693983)
expect_equal(dim(expand(gChain(grl.unlist(grl2)[1:500], grl.unlist(grl1))))[2], 3095693983)
## shift.x = FALSE, shift.y = FALSE
expect_equal(dim(expand(gChain(grl.unlist(grl2)), shift.x=FALSE, shift.y=FALSE))[1], 3095693983)
expect_equal(dim(expand(gChain(grl.unlist(grl2)), shift.x=FALSE, shift.y=FALSE))[2], 3095693983)
## shift.x = TRUE, shift.y = FALSE
expect_equal(dim(expand(gChain(grl.unlist(grl2)), shift.x=TRUE, shift.y=FALSE))[1], 3095693983)
expect_equal(dim(expand(gChain(grl.unlist(grl2)), shift.x=TRUE, shift.y=FALSE))[2], 3095693983)
})
test_that('testing values() works', {
## it looks like this is always an empty data.frame()
expect_equal(values(gChain(grl.unlist(grl2))), data.frame())
expect_equal(values(gChain(gr2, gr2)), data.frame())
})
test_that('testing t() works', {
expect_true(is(t(gChain()), 'gChain'))
})
test_that('testing breaks() works', {
### BUG
expect_error(breaks(gChain())) ## adjustment would result in ranges with negative widths
expect_equal(breaks(gChain(grl.unlist(grl2))), GRangesList())
#### Error in gr.start(x@.galy, 2) - 1 :
#### adjustment would result in ranges with negative widths ### happens because 'clip'
## en = pmin(en, end(x))
## st = pmax(st, start(x))
##
expect_equal(breaks(gChain(grl.unlist(grl2)[1:500], grl.unlist(grl1))), GRangesList())
##
## rev=TRUE
expect_equal(breaks(gChain(grl.unlist(grl2)[1:500], grl.unlist(grl1)), rev=TRUE), GRangesList())
##
expect_equal(breaks(gChain(gr, gr)), GRangesList())
expect_equal(breaks(gChain(example_genes)), GRangesList())
## if (!inherits(x, 'gChain')){ ... looks like checked by S4
expect_error(breaks('foo'))
## Error in (function (classes, fdef, mtable) :
## unable to find an inherited method for function ‘breaks’ for signature ‘"character"
expect_error(breaks(data.table()))
## Error in (function (classes, fdef, mtable) :
## unable to find an inherited method for function ‘breaks’ for signature ‘"data.table"’
})
## cn
test_that('testing cn() works', {
expect_equal(length(cn(gChain(grl.unlist(grl2)))), 1029)
test = grl2
names(test) = NULL
expect_equal(length(cn(gChain(grl.unlist(grl2)))), 1029)
expect_equal(length(cn(gChain(grl.unlist(grl2)), rev=TRUE)), 1029)
})
## setMethod('[', 'gChain', function(x, i){
test_that('testing [ works', {
expect_true(is(gChain()[1], 'gChain'))
## Error: subscript contains out-of-bounds indices
expect_error(gChain()[2])
})
## spChain
test_that('testing spChain() works', {
expect_true(is(spChain(grl2[1:3]), 'gChain'))
expect_equal(width(si2gr(seqinfo(spChain(grl2[1:3]))$y)[1]), 2)
## if (is.null(names(grl))){
foo = grl2
names(foo) = NULL
expect_true(is(spChain(foo[1:3]), 'gChain'))
expect_equal(width(si2gr(seqinfo(spChain(foo[1:3]))$y)[1]), 2)
})
test_that('testing gSubset() works', {
expect_error( gSubset(c('foo')))
expect_equal(length(gSubset(gChain())), 1)
})
## paChain()
test_that('testing paChain() works', {
s1 = DNAString("ACTTCACCAGCTCCCTGGCGGTAAGTTGATCAAAGGAAACGCAAAGTTTTCAAG")
s2 = DNAString("GTTTCACTACTTCCTTTCGGGTAAGTAAATATATAAATATATAAAAATATAATTTTCATC")
expect_equal(dim(paChain('ACTTCACCAGCTCCCTGGCGGTAAGTTGATCAAAGGAAACGCAAAGTTTTCAAG', 'GTTTCACTACTTCCTTTCGGGTAAGTAAATATATAAATATATAAAAATATAATTTTCATC'))[1], 54)
expect_equal(dim(paChain('ACTTCACCAGCTCCCTGGCGGTAAGTTGATCAAAGGAAACGCAAAGTTTTCAAG', 'GTTTCACTACTTCCTTTCGGGTAAGTAAATATATAAATATATAAAAATATAATTTTCATC'))[2], 60)
expect_equal(dim(suppressWarnings(paChain(s1, s2)))[1], 54)
expect_equal(dim(suppressWarnings(paChain(s1, s2)))[2], 60)
##
## if (inherits(seq1, 'factor')){
factor1 = factor("ACTTCACCAGCTCCCTGGCGGTAAGTTGATCAAAGGAAACGCAAAGTTTTCAAG")
factor2 = factor("GTTTCACTACTTCCTTTCGGGTAAGTAAATATATAAATATATAAAAATATAATTTTCATC")
expect_equal(dim(suppressWarnings(paChain(factor1, factor2)))[1], 54)
expect_equal(dim(suppressWarnings(paChain(factor1, factor2)))[2], 60)
## score.thresh
expect_equal(dim(suppressWarnings(paChain(factor1, factor2, score.thresh = 5000)))[1], 54)
expect_equal(dim(suppressWarnings(paChain(factor1, factor2, score.thresh = 5000)))[2], 60)
## pintersect
expect_equal(dim(suppressWarnings(paChain(factor1, factor2, pintersect=TRUE, verbose=TRUE)))[1], 54)
expect_equal(dim(suppressWarnings(paChain(factor1, factor2, pintersect=TRUE, verbose=TRUE)))[2], 60)
##
## paChain(factor1, factor2, both.strands=TRUE)
## Error in as.vector(x, mode = "character") :
## no method for coercing this S4 class to a vector
##
# reference sequence
# standardseq = AAString("MARKSLEMSIR")
# query sequences
# seq1 = AAString("MARKSLEMSER")
# seq2 = AAString("MDRKSLEMSER")
# seq3 = AAString("MDRKSAEMSER")
# seq4 = AAString("MARKSLEMSIR")
proteinseq1 = AAString("MDRKSAEMSER")
proteinseq2 = AAString("MDRKSLEMSER")
expect_equal(dim(suppressWarnings(paChain(proteinseq1, proteinseq2)))[1], 11)
expect_equal(dim(suppressWarnings(paChain(proteinseq1, proteinseq2)))[2], 11)
## assume.dna=FALSE
expect_equal(dim(paChain('MDRKSAEMSER', 'MDRKSLEMSER', assume.dna=FALSE))[1], 11)
expect_equal(dim(paChain('MDRKSAEMSER', 'MDRKSLEMSER', assume.dna=FALSE))[2], 11)
## Error in .Call2("new_XString_from_CHARACTER", classname, x, start(solved_SEW), :
## key 69 (char 'E') not in lookup table
expect_error(dim(paChain('MDRKSAEMSER', 'MDRKSLEMSER')))
expect_error(paChain(AAString("MDRKSAEMSER"), 'ACCCT'))
##
fact1 = "ACTTCACCAGCTCCCTGGCGGT"
fact2 = "GTTTCACTACTTCCTTTCGGGTAAGTAAATATATAAATATATAAAAATATAATTTTCATC"
expect_equal(dim(suppressWarnings(paChain(fact1, fact2)))[1], 22)
expect_equal(dim(suppressWarnings(paChain(fact1, fact2)))[2], 60)
## ## GRanges corresponding to seq1, MUST be of same width, length, and names as seq1
##
## Error in paChain(fact1, fact2, gr1 = example_dnase[1]) :
## Widths of gr1 and seq1 not compatible
expect_error(paChain(fact1,fact2, gr1=example_dnase[1]))
## Error in paChain(fact1, fact2, gr2 = example_dnase[1]) :
## Widths of gr2 and seq1 not compatible
expect_error(paChain(fact1,fact2, gr2=example_dnase[1]))
##
## BUG
## paChain(fact1, fact2, gr1 = GRanges('2:50-71'), gr3 = GRanges('3:50-71'))
##
fa1 = "A"
fa2 = "GTTTCACTACTTCCTTTCGGGTAAGTAAATATATAAATATATAAAAATATAATTTTCATC"
expect_equal(dim(suppressWarnings(paChain(fa1, fa2)))[1], 1)
expect_equal(dim(suppressWarnings(paChain(fa1, fa2)))[2], 60)
f1 = "ACTTCACCAGCTCCCTGGCGGT"
f2 = "C"
expect_equal(dim(suppressWarnings(paChain(f1, f2)))[1], 22)
expect_equal(dim(suppressWarnings(paChain(f1, f2)))[2], 1)
## *** caught segfault ***
## address 0x7f7fc7800000, cause 'memory not mapped'
## pairwiseAlignment(seq1, seq2)
ff1 = "ACTTCACCAGCTCCCTGGCGGT"
ff2 = ""
## Error in paChain(ff1, ff2) :
## Either seq1 and/or seq2 is of width 0. This will result in an error with pairwiseAlignment(seq1, seq2).
expect_error(paChain(ff1, ff2))
##
fact1 = "ACTTCACCAGCTCCCTGGCGGT"
fact2 = "GTTTCACTACTTCCTTTCGGGTAAGTAAATATATAAATATATAAAAATATAATTTTCATC"
expect_equal(dim(suppressWarnings(paChain(fact1, fact2, sn1 = c('one', 'two', 'three', 'four'), sn2 = c('one', 'one', 'one'))))[1], 60)
expect_equal(dim(suppressWarnings(paChain(fact1, fact2, sn1 = c('one', 'two', 'three', 'four'), sn2 = c('one', 'one', 'one'))))[2], 60)
})
library(bamUtils)
example_bam = 'smallHCC1143BL.bam' ### all tests below are specific to this BAM, and will fail otherwise
example_bai = 'smallHCC1143BL.bam.bai'
## cgChain()
test_that('testing cgChain() works', {
expect_equal(dim(cgChain('3M1I3M1D5M'))[1], 12)
expect_equal(dim(cgChain('3M1I3M1D5M'))[2], 12)
## GRanges
gr2$cigar = c('3M', '8M2I27M')
## Error in aggregate.data.frame(as.data.frame(x), ...) :
## GRanges
## else if (inherits(cigar, 'GRanges')) {
ff = read.bam(example_bam, all=TRUE)
expect_equal(dim(cgChain(ff[[1]]))[1], 202)
expect_equal(dim(cgChain(ff[[1]]))[2], 3101804739)
## if (any(ix <- is.na(values(cigar)$cigar))){
grff = ff[[1]]
grff$cigar[2] = NA
expect_equal(dim(cgChain(grff))[1], 101)
expect_equal(dim(cgChain(grff))[2], 3101804739)
## data.table
## dtt = gr2dt(ff[[1]])
## expect_equal(dim(cgChain(dtt))[1], 101)
## expect_equal(dim(cgChain(dtt))[2], 10467)
### sure about 'sn' parameter ....
expect_equal(dim(cgChain('3M1I3M1D5M', sn=2))[1], 12)
expect_equal(dim(cgChain('3M1I3M1D5M', sn=2))[2], 12)
expect_equal(dim(cgChain('3M1I3M1D5M', sn='mpos'))[1], 12)
expect_equal(dim(cgChain('3M1I3M1D5M', sn='mpos'))[2], 12)
})
## maChain()
test_that('testing maChain() works', {
proteinseq1 = AAString("MDRKSAEMSER")
## proteinseq2 = AAString("MDRKSLEMSER")
expect_equal(dim(maChain(grl=NULL, proteinseq1))[1], 11)
expect_equal(dim(maChain(grl=NULL, proteinseq1))[2], 1)
})
## txChain
test_that('testing txChain() works', {
## GRangesList input
expect_equal(dim(txChain(grl2))[1], 3095693983)
expect_equal(dim(txChain(grl2))[2], 502)
## GRanges input
expect_true(is(txChain(example_dnase), 'gChain'))
## val
labels = c(rep('hey', 10000))
expect_equal(dim(txChain(example_dnase, val=labels))[1], 3095693983)
expect_equal(dim(txChain(example_dnase, val=labels))[2], 6070884)
## Error: val data.frame must correspond to grl, i.e. have nrows = length(grl)
expect_error(txChain(example_dnase, val = c("foo", "bar")))
## txchain
txchain_labels = c(rep('foo', 251))
expect_equal(dim(txChain(example_dnase, txchain_labels))[1], 3095693983)
expect_equal(dim(txChain(example_dnase, txchain_labels))[2], 6070884)
## exonFrame.field
expect_true(is(txChain(grl2, exonFrame.field = 'bin'), 'gChain'))
expect_equal(dim(txChain(grl2, exonFrame.field = 'bin'))[1], 3095693983)
expect_equal(dim(txChain(grl2, exonFrame.field = 'bin'))[2], 761)
## translate
expect_equal(dim(txChain(example_dnase, translate=TRUE))[1], 3095693983)
expect_equal(dim(txChain(example_dnase, translate=TRUE))[2], 2023628)
})
### duplicate
test_that('testing duplicate() works', {
## default
gChain_duplicate = duplicate(gr2)
expect_equal(dim(gChain_duplicate)[1], 25)
expect_equal(dim(gChain_duplicate)[2], 37)
foo = GRanges(1, IRanges(c(1, 8), c(10, 14)), strand=c('+','+'))
## Error in duplicate(foo) : Error: Input ranges must be nonoverlapping
expect_error(duplicate(foo))
expect_error(duplicate(example_genes))
expect_true(is(duplicate(grl.unlist(grl2)), 'gChain'))
})
### copy
test_that('testing copy() works', {
expect_true(is(copy(grl.unlist(grl2)), 'gChain'))
expect_equal(length(copy(grl.unlist(grl2))), 1)
## if (any(strand(from) == '*')){
foo = example_dnase
strand(foo) = '*'
expect_true(is(copy(foo), 'gChain'))
})
### delete
test_that('testing delete() works', {
expect_true(is(delete(grl.unlist(grl2)), 'gChain'))
expect_equal(length(delete(grl.unlist(grl2))), 1)
})
### invert
test_that('testing invert() works', {
expect_true(is(invert(grl.unlist(grl2)), 'gChain'))
expect_equal(length(invert(grl.unlist(grl2))), 1)
})
test_that('testing permute() works', {
expect_error(permute(grl2), NA) ## check works
expect_equal(length(permute(grl2)), 1)
## if (any(strand(c.gr)=='*'))
foo = grl2
foo = GRangesList(lapply(foo, function(x) {strand(x) = "*"; return(x)}))
expect_equal(dim(permute(foo))[1], 3095693983) ## outputs warning message, In permute(foo) : Converting * strands to +
expect_equal(dim(permute(foo))[2], 3095693983)
gr_overlap = GRanges(1, IRanges(c(1, 8), c(10, 14)), strand=c('+','+'))
## Error: Intervals describing permutation cycles have to be disjoint
expect_error(permute(gr_overlap))
})
## rearrange()
test_that('testing rearrange() works', {
## Error in gr.flipstrand(event[-1]) : Error: GRanges input only
expect_error(rearrange(grl1))
## if (any(strand(event) == '*')){
## Error in rearrange(foo) :
## bp1 and bp2 must be signed intervals (ie either + or -)
foo = grl.unlist(grl2)
strand(foo) = '*'
expect_error(rearrange(foo))
## if (sum(width(reduce(event))) != sum(width(event))){
## event cannot have duplicates with respect to location and strand
gr_overlap = GRanges(1, IRanges(c(1, 8), c(10, 14)), strand=c('+','+'))
expect_error(rearrange(event = gr_overlap))
## default
expect_equal(dim(rearrange(grl.unlist(grl1)))[1], 3095693983)
expect_equal(dim(rearrange(grl.unlist(grl1)))[2], 3091997226)
## closed = TRUE
expect_equal(dim(rearrange(grl.unlist(grl1), closed=FALSE))[1], 3095693983)
expect_equal(dim(rearrange(grl.unlist(grl1), closed=FALSE))[2], 2976729654)
## retain
expect_equal(dim(rearrange(grl.unlist(grl1), retain=50))[1], 3095693983)
expect_equal(dim(rearrange(grl.unlist(grl1), retain=50))[2], 3091997226)
## filter.tel = TRUE
expect_equal(dim(rearrange(grl.unlist(grl1), filter.tel = TRUE))[1], 3095693983)
expect_equal(dim(rearrange(grl.unlist(grl1), filter.tel = TRUE))[2], 3091997226)
})
test_that('testing bfb() works', {
## stop('w and wd must be positive')
expect_error(bfb(w=-.05))
expect_error(bfb(3), NA) ## check runs
### even setting set.seed(), the dim() varies
expect_true(is(bfb(3), 'gChain'))
})
### utility functions
test_that('testing vec2ir() works', {
expect_equal(width(vec2ir(c(1, 2, 2, 2))[1]), 2)
expect_equal(width(vec2ir(c(1, 2, 2, 2))[2]), 1)
expect_equal(width(vec2ir(c(1, 2, 2, 2))[3]), 1)
})
test_that('testing ir2vec() works', {
gr = GRanges(1, IRanges(c(3,7,13), c(5,9,16)), strand=c('+','-','-'), seqinfo=Seqinfo("1", 25), name=c("A","B","C"))
expect_equal(length(ir2vec(gr)), 10)
expect_equal(ir2vec(gr)[1], 3)
expect_equal(ir2vec(gr)[10], 16)
expect_equal(length(ir2vec(i2, each=c(2, 4, 6))), 120)
})
test_that('testing gCat() works', {
expect_true(is(gCat(), 'gChain'))
expect_true(is(gCat(gCat(), gCat()), 'gChain'))
foo1 = gChain(grl.unlist(grl1), grl.unlist(grl2)[1:500])
foo2 = gChain(example_dnase[1:200])
expect_true(is(gCat(foo1, foo2), 'gChain'))
})
test_that('testing gUnique() works', {
expect_true(is(gUnique(gChain()), 'gChain'))
})
test_that('testing squeeze() works', {
gr = GRanges(1, IRanges(c(3,7,13), c(5,9,16)), strand=c('+','-','-'), seqinfo=Seqinfo("1", 25), name=c("A","B","C"))
expect_error(squeeze(gr))
ir1 = IRanges(c(3,7,13), c(5,9,16))
expect_equal(width(squeeze(ir1))[1], 3)
expect_equal(width(squeeze(ir1))[3], 4)
expect_equal(squeeze(IRanges()), IRanges())
irlength1 = IRanges(c(1300), c(1600))
expect_equal(as.data.frame(squeeze(irlength1))$width, 301)
})
### grl.split()
test_that('grl.split() works', {
expect_true(is(grl.split(grl2), 'GRangesList'))
expect_equal(length(grl.split(grl2)), 497)
})
## levapply()
test_that('levapply() works', {
gr = GRanges(1, IRanges(c(3,7,13), c(5,9,16)), strand=c('+','-','-'), seqinfo=Seqinfo("1", 25), name=c("A","B","C"))
foo = levapply(width(gr), as.character(seqnames(gr)), function(x) if (length(x)>1) cumsum(c(0, x[1:(length(x)-1)])) else return(0))
expect_equal(foo, c(0, 3, 6))
})
## seqinfo2gr()
test_that('seqinfo2gr() works', {
gr = GRanges(1, IRanges(c(3,7,13), c(5,9,16)), strand=c('+','-','-'), seqinfo=Seqinfo("1", 25), name=c("A","B","C"))
expect_equal(width(seqinfo2gr(gr)), 25)
expect_equal(length(seqinfo2gr(si)), 25)
expect_equal(length(seqinfo2gr(si, strip.empty=TRUE)), 25)
})
## dedup()
test_that('dedup() works', {
expect_equal(dedup(c(rep(2, 10.5), rep(3, 20)))[30], "3.20")
})
## gr.pad()
test_that('gr.pad() works', {
expect_equal(width(gr.pad(gr2, 10)[1]), 16)
expect_equal(width(gr.pad(gr2, 10)[2]), 24)
})
## gr.refactor()
test_that('gr.refactor() works', {
expect_equal(as.character(seqnames(gr.refactor(gr2, sn = c('2', '2'))))[1], '2')
expect_equal(as.character(seqnames(gr.refactor(gr2, sn = c('chr2', '2'))))[1], 'chr2')
expect_equal(as.character(seqnames(gr.refactor(gr2, sn = c('chr2', 'foo'))))[2], 'foo')
## if (is.factor(sn)){
expect_equal(as.character(seqnames(gr.refactor(gr2, sn = factor(c('2', '2')))))[1], '2')
expect_equal(as.character(seqnames(gr.refactor(gr2, sn = factor(c('chr2', '2')))))[1], 'chr2')
expect_equal(as.character(seqnames(gr.refactor(gr2, sn = factor(c('chr2', 'foo')))))[2], 'foo')
})
## gr.tostring()
test_that('gr.tostring() works', {
expect_true(is(gr.tostring(gr2), 'character'))
})
mskilab/gChain documentation built on Sept. 28, 2022, 3:45 p.m.
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library(gChain)
library(testthat)
library(gUtils)
library(gTrack)
Sys.setenv(DEFAULT_BSGENOME = "BSgenome.Hsapiens.UCSC.hg19::Hsapiens")
gr = GRanges(1, IRanges(c(3,7,13), c(5,9,16)), strand=c('+','-','-'), seqinfo=Seqinfo("1", 25), name=c("A","B","C"))
gr2 = GRanges(1, IRanges(c(1,9), c(6,14)), strand=c('+','-'), seqinfo=Seqinfo("1", 25), field=c(1,2))
dt = data.table(seqnames=1, start=c(2,5,10), end=c(3,8,15))
i1 = IRanges(c(3,7,13), c(5,9,16))
i2 = IRanges(c(1,9, 32), c(6,14, 45))
test_that('testing gChain() works', {
expect_true(is(gChain(), 'gChain'))
expect_equal(length(gChain()), 1)
expect_equal(width(gChain()$x), 0)
### dim()
expect_equal(dim(gChain())[1], 0)
expect_equal(dim(gChain())[2], 0)
### links()
expect_equal(width(links(gChain())$x), 0)
expect_equal(width(links(gChain())$y), 0)
### values()
expect_equal(values(gChain()), data.frame())
## c()
expect_equal(values(c(gChain(gr), gChain(gr2))), data.frame())
expect_equal(values(gChain(x = si, y = si)), data.frame())
expect_equal(values(gChain(x = GRanges(), y = NULL)), data.frame())
expect_equal(values(gChain(x = NULL, y = GRanges())), data.frame())
expect_equal(values(c(gChain())), data.frame())
## Error: At least one of the objects to be concatanted is not a gChain
expect_error(c(gChain(gr), c('foo')))
## check 'show()' works
expect_error(show(gChain()), NA)
## if (length(x)>0 & length(y)>0 & length(x) != length(y)){
expect_error(gChain(gr, gr2))
## if (is(x, 'IRanges')){
expect_equal(dim(gChain(x = i1))[1], 16)
expect_equal(dim(gChain(x = i1))[2], 16)
## if (is(y, 'IRanges')){
expect_equal(dim(gChain(y = i2))[1], 45)
expect_equal(dim(gChain(y = i2))[2], 45)
## Error in validObject(.Object) :
## invalid class “gChain” object: 1: All intervals pairs must have a single scale
## invalid class “gChain” object: 2: Scales not consistent with interval pair widths and .pad.left / .pad.right properties.
expect_error(gChain(i2, i1))
## if (!is(x, 'GRanges') | !is(y, 'GRanges')){
## Error: inputs to gChain() must be of the type GRanges
expect_error(gChain(grl2))
expect_equal(dim(gChain(gr[1:2], gr2, val = 42))[1], 25)
## if (ncol(val)>0 & nrow(val)==1){
expect_equal(dim(gChain(gr[1:2], gr2, val = data.frame(c(42))))[1], 25)
## if (is.vector(val)){
expect_equal(dim(gChain(gr[1:2], gr2, val = c(42, 13)))[1], 25)
## x = NULL, y = NULL, pad.left = 0, pad.right = 0, scale = NULL, val = data.frame())
## if (is.null(scale)){
expect_equal(dim((gChain(gr2, scale=1)))[1], 25)
## what does scale < 0 mean?
expect_equal(dim((gChain(gr2, scale=-1)))[1], 25)
})
test_that('testing gMultiply() works', {
gc1 = gChain(gr, gr)
gc2 = gChain(gr, gr)
gc2 = gMultiply(gc1, gc2)
## expect_equal(gc1, gc2)
expect_equal(gMultiply(gc1, gc2), gMultiply(gc2, gc1))
## empty GRanges()
foo1 = gChain(grl.unlist(grl1), grl.unlist(grl2)[1:500])
foo2 = gChain(example_dnase[1:200])
multiplied = gMultiply(foo1, foo2)
expect_equal(multiplied, GRanges())
})
test_that('testing scale() works', {
expect_equal(scale(gChain()), 1)
})
test_that('testing lift() works', {
expect_equal(length(gChain()), 1)
foo = gChain(grl.unlist(grl2))
expect_equal(length(lift(foo, grl.unlist(grl2))), 502)
expect_equal(length(lift(foo, grl.unlist(grl2), split.grl = TRUE)), 502)
## if (!(format %in% c('GRanges', 'df', 'df.all', 'matrix', 'GRangesList', 'gTrack'))){
expect_error(length(lift(foo, grl.unlist(grl2), format='foobar')))
expect_error(lift(foo, c(1))) ## Error in .local(.Object, x, ...) : Error: x must be Granges object
expect_equal(length(lift(foo, grl2)), 251)
expect_equal(length(lift(foo, IRanges(c(3,7,13), c(5,9,16)))), 0)
## data.frame
expect_true(is(lift(foo, grl.unlist(grl2), format='df'), 'data.frame'))
expect_equal(dim(lift(foo, grl.unlist(grl2), format='df'))[1], 502)
expect_equal(dim(lift(foo, grl.unlist(grl2), format='df'))[2], 4)
## GRanges
expect_equal(length(lift(foo, grl.unlist(grl2), format='GRanges')), 502)
expect_true(is(lift(foo, grl.unlist(grl2), format='GRanges'), 'GRanges'))
## gTrack
expect_equal(dim(lift(foo, grl.unlist(grl2), format='gTrack'))[1], 502)
expect_equal(dim(lift(foo, grl.unlist(grl2), format='gTrack'))[2], 4)
## matrix
expect_equal(dim(lift(foo, grl.unlist(grl2), format='matrix'))[1], 502)
expect_equal(dim(lift(foo, grl.unlist(grl2), format='matrix'))[2], 4)
##
expect_true(is(lift(gChain(example_genes), gTrack(example_genes), format='gTrack'), 'gTrack'))
## if (is(x, 'gTrack')){
## if (length(x)>1){
expect_true(is(lift(gChain(example_genes), c(gTrack(example_genes), gTrack(example_dnase), gTrack(grl.unlist(grl2))), format='gTrack'), 'gTrack'))
})
test_that('testing scale()) works', {
expect_equal(scale(gChain()), 1)
})
test_that('testing pads() works', {
expect_equal(pads(gChain())$pad.left, 0)
expect_equal(pads(gChain())$pad.right, 0)
})
test_that('testing genomes() works', {
expect_equal(width(genomes(gChain())$x), 0)
expect_equal(width(genomes(gChain())$y), 0)
})
test_that('testing "*" works', {
## identity multiplication
## setMethod("*", signature(e1 = "gChain", e2 = "GRanges"), function(e1, e2)
gc1 = gChain(gr,gr)
gc2 = gChain(gr,gr)
## gc2 = gc1 * gc2
## expect_equal(gc1, gc2)
expect_equal((gc1 * gc2), (gc2 * gc1))
## with GRList
## setMethod("*", signature(e1 = "gChain", e2 = "GRangesList"), function(e1, e2)
expect_equal(length(gc1 * grl2), 0)
## with GRanges
expect_equal(length(gc1 * gr2), 3)
})
test_that('testing expand() works', {
### setMethod("expand", signature(x = "gChain"), function(x, space = NULL, shift.x = FALSE, shift.y = TRUE)
expect_true(is(expand(gChain(grl.unlist(grl2))), 'gChain'))
expect_equal(dim(expand(gChain(grl.unlist(grl2))))[1], 3095693983)
expect_equal(dim(expand(gChain(grl.unlist(grl2))))[2], 3095693983)
##
expect_equal(dim(expand(gChain(grl.unlist(grl2)[1:25], grl.unlist(grl1)[1:25])))[1], 3095693983)
expect_equal(dim(expand(gChain(grl.unlist(grl2)[1:25], grl.unlist(grl1)[1:25])))[2], 3095693983)
expect_equal(dim(expand(gChain(grl.unlist(grl2)[1:500], grl.unlist(grl1))))[1], 3095693983)
expect_equal(dim(expand(gChain(grl.unlist(grl2)[1:500], grl.unlist(grl1))))[2], 3095693983)
## shift.x = FALSE, shift.y = FALSE
expect_equal(dim(expand(gChain(grl.unlist(grl2)), shift.x=FALSE, shift.y=FALSE))[1], 3095693983)
expect_equal(dim(expand(gChain(grl.unlist(grl2)), shift.x=FALSE, shift.y=FALSE))[2], 3095693983)
## shift.x = TRUE, shift.y = FALSE
expect_equal(dim(expand(gChain(grl.unlist(grl2)), shift.x=TRUE, shift.y=FALSE))[1], 3095693983)
expect_equal(dim(expand(gChain(grl.unlist(grl2)), shift.x=TRUE, shift.y=FALSE))[2], 3095693983)
})
test_that('testing values() works', {
## it looks like this is always an empty data.frame()
expect_equal(values(gChain(grl.unlist(grl2))), data.frame())
expect_equal(values(gChain(gr2, gr2)), data.frame())
})
test_that('testing t() works', {
expect_true(is(t(gChain()), 'gChain'))
})
test_that('testing breaks() works', {
### BUG
expect_error(breaks(gChain())) ## adjustment would result in ranges with negative widths
expect_equal(breaks(gChain(grl.unlist(grl2))), GRangesList())
#### Error in gr.start(x@.galy, 2) - 1 :
#### adjustment would result in ranges with negative widths ### happens because 'clip'
## en = pmin(en, end(x))
## st = pmax(st, start(x))
##
expect_equal(breaks(gChain(grl.unlist(grl2)[1:500], grl.unlist(grl1))), GRangesList())
##
## rev=TRUE
expect_equal(breaks(gChain(grl.unlist(grl2)[1:500], grl.unlist(grl1)), rev=TRUE), GRangesList())
##
expect_equal(breaks(gChain(gr, gr)), GRangesList())
expect_equal(breaks(gChain(example_genes)), GRangesList())
## if (!inherits(x, 'gChain')){ ... looks like checked by S4
expect_error(breaks('foo'))
## Error in (function (classes, fdef, mtable) :
## unable to find an inherited method for function ‘breaks’ for signature ‘"character"
expect_error(breaks(data.table()))
## Error in (function (classes, fdef, mtable) :
## unable to find an inherited method for function ‘breaks’ for signature ‘"data.table"’
})
## cn
test_that('testing cn() works', {
expect_equal(length(cn(gChain(grl.unlist(grl2)))), 1029)
test = grl2
names(test) = NULL
expect_equal(length(cn(gChain(grl.unlist(grl2)))), 1029)
expect_equal(length(cn(gChain(grl.unlist(grl2)), rev=TRUE)), 1029)
})
## setMethod('[', 'gChain', function(x, i){
test_that('testing [ works', {
expect_true(is(gChain()[1], 'gChain'))
## Error: subscript contains out-of-bounds indices
expect_error(gChain()[2])
})
## spChain
test_that('testing spChain() works', {
expect_true(is(spChain(grl2[1:3]), 'gChain'))
expect_equal(width(si2gr(seqinfo(spChain(grl2[1:3]))$y)[1]), 2)
## if (is.null(names(grl))){
foo = grl2
names(foo) = NULL
expect_true(is(spChain(foo[1:3]), 'gChain'))
expect_equal(width(si2gr(seqinfo(spChain(foo[1:3]))$y)[1]), 2)
})
test_that('testing gSubset() works', {
expect_error( gSubset(c('foo')))
expect_equal(length(gSubset(gChain())), 1)
})
## paChain()
test_that('testing paChain() works', {
s1 = DNAString("ACTTCACCAGCTCCCTGGCGGTAAGTTGATCAAAGGAAACGCAAAGTTTTCAAG")
s2 = DNAString("GTTTCACTACTTCCTTTCGGGTAAGTAAATATATAAATATATAAAAATATAATTTTCATC")
expect_equal(dim(paChain('ACTTCACCAGCTCCCTGGCGGTAAGTTGATCAAAGGAAACGCAAAGTTTTCAAG', 'GTTTCACTACTTCCTTTCGGGTAAGTAAATATATAAATATATAAAAATATAATTTTCATC'))[1], 54)
expect_equal(dim(paChain('ACTTCACCAGCTCCCTGGCGGTAAGTTGATCAAAGGAAACGCAAAGTTTTCAAG', 'GTTTCACTACTTCCTTTCGGGTAAGTAAATATATAAATATATAAAAATATAATTTTCATC'))[2], 60)
expect_equal(dim(suppressWarnings(paChain(s1, s2)))[1], 54)
expect_equal(dim(suppressWarnings(paChain(s1, s2)))[2], 60)
##
## if (inherits(seq1, 'factor')){
factor1 = factor("ACTTCACCAGCTCCCTGGCGGTAAGTTGATCAAAGGAAACGCAAAGTTTTCAAG")
factor2 = factor("GTTTCACTACTTCCTTTCGGGTAAGTAAATATATAAATATATAAAAATATAATTTTCATC")
expect_equal(dim(suppressWarnings(paChain(factor1, factor2)))[1], 54)
expect_equal(dim(suppressWarnings(paChain(factor1, factor2)))[2], 60)
## score.thresh
expect_equal(dim(suppressWarnings(paChain(factor1, factor2, score.thresh = 5000)))[1], 54)
expect_equal(dim(suppressWarnings(paChain(factor1, factor2, score.thresh = 5000)))[2], 60)
## pintersect
expect_equal(dim(suppressWarnings(paChain(factor1, factor2, pintersect=TRUE, verbose=TRUE)))[1], 54)
expect_equal(dim(suppressWarnings(paChain(factor1, factor2, pintersect=TRUE, verbose=TRUE)))[2], 60)
##
## paChain(factor1, factor2, both.strands=TRUE)
## Error in as.vector(x, mode = "character") :
## no method for coercing this S4 class to a vector
##
# reference sequence
# standardseq = AAString("MARKSLEMSIR")
# query sequences
# seq1 = AAString("MARKSLEMSER")
# seq2 = AAString("MDRKSLEMSER")
# seq3 = AAString("MDRKSAEMSER")
# seq4 = AAString("MARKSLEMSIR")
proteinseq1 = AAString("MDRKSAEMSER")
proteinseq2 = AAString("MDRKSLEMSER")
expect_equal(dim(suppressWarnings(paChain(proteinseq1, proteinseq2)))[1], 11)
expect_equal(dim(suppressWarnings(paChain(proteinseq1, proteinseq2)))[2], 11)
## assume.dna=FALSE
expect_equal(dim(paChain('MDRKSAEMSER', 'MDRKSLEMSER', assume.dna=FALSE))[1], 11)
expect_equal(dim(paChain('MDRKSAEMSER', 'MDRKSLEMSER', assume.dna=FALSE))[2], 11)
## Error in .Call2("new_XString_from_CHARACTER", classname, x, start(solved_SEW), :
## key 69 (char 'E') not in lookup table
expect_error(dim(paChain('MDRKSAEMSER', 'MDRKSLEMSER')))
expect_error(paChain(AAString("MDRKSAEMSER"), 'ACCCT'))
##
fact1 = "ACTTCACCAGCTCCCTGGCGGT"
fact2 = "GTTTCACTACTTCCTTTCGGGTAAGTAAATATATAAATATATAAAAATATAATTTTCATC"
expect_equal(dim(suppressWarnings(paChain(fact1, fact2)))[1], 22)
expect_equal(dim(suppressWarnings(paChain(fact1, fact2)))[2], 60)
## ## GRanges corresponding to seq1, MUST be of same width, length, and names as seq1
##
## Error in paChain(fact1, fact2, gr1 = example_dnase[1]) :
## Widths of gr1 and seq1 not compatible
expect_error(paChain(fact1,fact2, gr1=example_dnase[1]))
## Error in paChain(fact1, fact2, gr2 = example_dnase[1]) :
## Widths of gr2 and seq1 not compatible
expect_error(paChain(fact1,fact2, gr2=example_dnase[1]))
##
## BUG
## paChain(fact1, fact2, gr1 = GRanges('2:50-71'), gr3 = GRanges('3:50-71'))
##
fa1 = "A"
fa2 = "GTTTCACTACTTCCTTTCGGGTAAGTAAATATATAAATATATAAAAATATAATTTTCATC"
expect_equal(dim(suppressWarnings(paChain(fa1, fa2)))[1], 1)
expect_equal(dim(suppressWarnings(paChain(fa1, fa2)))[2], 60)
f1 = "ACTTCACCAGCTCCCTGGCGGT"
f2 = "C"
expect_equal(dim(suppressWarnings(paChain(f1, f2)))[1], 22)
expect_equal(dim(suppressWarnings(paChain(f1, f2)))[2], 1)
## *** caught segfault ***
## address 0x7f7fc7800000, cause 'memory not mapped'
## pairwiseAlignment(seq1, seq2)
ff1 = "ACTTCACCAGCTCCCTGGCGGT"
ff2 = ""
## Error in paChain(ff1, ff2) :
## Either seq1 and/or seq2 is of width 0. This will result in an error with pairwiseAlignment(seq1, seq2).
expect_error(paChain(ff1, ff2))
##
fact1 = "ACTTCACCAGCTCCCTGGCGGT"
fact2 = "GTTTCACTACTTCCTTTCGGGTAAGTAAATATATAAATATATAAAAATATAATTTTCATC"
expect_equal(dim(suppressWarnings(paChain(fact1, fact2, sn1 = c('one', 'two', 'three', 'four'), sn2 = c('one', 'one', 'one'))))[1], 60)
expect_equal(dim(suppressWarnings(paChain(fact1, fact2, sn1 = c('one', 'two', 'three', 'four'), sn2 = c('one', 'one', 'one'))))[2], 60)
})
library(bamUtils)
example_bam = 'smallHCC1143BL.bam' ### all tests below are specific to this BAM, and will fail otherwise
example_bai = 'smallHCC1143BL.bam.bai'
## cgChain()
test_that('testing cgChain() works', {
expect_equal(dim(cgChain('3M1I3M1D5M'))[1], 12)
expect_equal(dim(cgChain('3M1I3M1D5M'))[2], 12)
## GRanges
gr2$cigar = c('3M', '8M2I27M')
## Error in aggregate.data.frame(as.data.frame(x), ...) :
## GRanges
## else if (inherits(cigar, 'GRanges')) {
ff = read.bam(example_bam, all=TRUE)
expect_equal(dim(cgChain(ff[[1]]))[1], 202)
expect_equal(dim(cgChain(ff[[1]]))[2], 3101804739)
## if (any(ix <- is.na(values(cigar)$cigar))){
grff = ff[[1]]
grff$cigar[2] = NA
expect_equal(dim(cgChain(grff))[1], 101)
expect_equal(dim(cgChain(grff))[2], 3101804739)
## data.table
## dtt = gr2dt(ff[[1]])
## expect_equal(dim(cgChain(dtt))[1], 101)
## expect_equal(dim(cgChain(dtt))[2], 10467)
### sure about 'sn' parameter ....
expect_equal(dim(cgChain('3M1I3M1D5M', sn=2))[1], 12)
expect_equal(dim(cgChain('3M1I3M1D5M', sn=2))[2], 12)
expect_equal(dim(cgChain('3M1I3M1D5M', sn='mpos'))[1], 12)
expect_equal(dim(cgChain('3M1I3M1D5M', sn='mpos'))[2], 12)
})
## maChain()
test_that('testing maChain() works', {
proteinseq1 = AAString("MDRKSAEMSER")
## proteinseq2 = AAString("MDRKSLEMSER")
expect_equal(dim(maChain(grl=NULL, proteinseq1))[1], 11)
expect_equal(dim(maChain(grl=NULL, proteinseq1))[2], 1)
})
## txChain
test_that('testing txChain() works', {
## GRangesList input
expect_equal(dim(txChain(grl2))[1], 3095693983)
expect_equal(dim(txChain(grl2))[2], 502)
## GRanges input
expect_true(is(txChain(example_dnase), 'gChain'))
## val
labels = c(rep('hey', 10000))
expect_equal(dim(txChain(example_dnase, val=labels))[1], 3095693983)
expect_equal(dim(txChain(example_dnase, val=labels))[2], 6070884)
## Error: val data.frame must correspond to grl, i.e. have nrows = length(grl)
expect_error(txChain(example_dnase, val = c("foo", "bar")))
## txchain
txchain_labels = c(rep('foo', 251))
expect_equal(dim(txChain(example_dnase, txchain_labels))[1], 3095693983)
expect_equal(dim(txChain(example_dnase, txchain_labels))[2], 6070884)
## exonFrame.field
expect_true(is(txChain(grl2, exonFrame.field = 'bin'), 'gChain'))
expect_equal(dim(txChain(grl2, exonFrame.field = 'bin'))[1], 3095693983)
expect_equal(dim(txChain(grl2, exonFrame.field = 'bin'))[2], 761)
## translate
expect_equal(dim(txChain(example_dnase, translate=TRUE))[1], 3095693983)
expect_equal(dim(txChain(example_dnase, translate=TRUE))[2], 2023628)
})
### duplicate
test_that('testing duplicate() works', {
## default
gChain_duplicate = duplicate(gr2)
expect_equal(dim(gChain_duplicate)[1], 25)
expect_equal(dim(gChain_duplicate)[2], 37)
foo = GRanges(1, IRanges(c(1, 8), c(10, 14)), strand=c('+','+'))
## Error in duplicate(foo) : Error: Input ranges must be nonoverlapping
expect_error(duplicate(foo))
expect_error(duplicate(example_genes))
expect_true(is(duplicate(grl.unlist(grl2)), 'gChain'))
})
### copy
test_that('testing copy() works', {
expect_true(is(copy(grl.unlist(grl2)), 'gChain'))
expect_equal(length(copy(grl.unlist(grl2))), 1)
## if (any(strand(from) == '*')){
foo = example_dnase
strand(foo) = '*'
expect_true(is(copy(foo), 'gChain'))
})
### delete
test_that('testing delete() works', {
expect_true(is(delete(grl.unlist(grl2)), 'gChain'))
expect_equal(length(delete(grl.unlist(grl2))), 1)
})
### invert
test_that('testing invert() works', {
expect_true(is(invert(grl.unlist(grl2)), 'gChain'))
expect_equal(length(invert(grl.unlist(grl2))), 1)
})
test_that('testing permute() works', {
expect_error(permute(grl2), NA) ## check works
expect_equal(length(permute(grl2)), 1)
## if (any(strand(c.gr)=='*'))
foo = grl2
foo = GRangesList(lapply(foo, function(x) {strand(x) = "*"; return(x)}))
expect_equal(dim(permute(foo))[1], 3095693983) ## outputs warning message, In permute(foo) : Converting * strands to +
expect_equal(dim(permute(foo))[2], 3095693983)
gr_overlap = GRanges(1, IRanges(c(1, 8), c(10, 14)), strand=c('+','+'))
## Error: Intervals describing permutation cycles have to be disjoint
expect_error(permute(gr_overlap))
})
## rearrange()
test_that('testing rearrange() works', {
## Error in gr.flipstrand(event[-1]) : Error: GRanges input only
expect_error(rearrange(grl1))
## if (any(strand(event) == '*')){
## Error in rearrange(foo) :
## bp1 and bp2 must be signed intervals (ie either + or -)
foo = grl.unlist(grl2)
strand(foo) = '*'
expect_error(rearrange(foo))
## if (sum(width(reduce(event))) != sum(width(event))){
## event cannot have duplicates with respect to location and strand
gr_overlap = GRanges(1, IRanges(c(1, 8), c(10, 14)), strand=c('+','+'))
expect_error(rearrange(event = gr_overlap))
## default
expect_equal(dim(rearrange(grl.unlist(grl1)))[1], 3095693983)
expect_equal(dim(rearrange(grl.unlist(grl1)))[2], 3091997226)
## closed = TRUE
expect_equal(dim(rearrange(grl.unlist(grl1), closed=FALSE))[1], 3095693983)
expect_equal(dim(rearrange(grl.unlist(grl1), closed=FALSE))[2], 2976729654)
## retain
expect_equal(dim(rearrange(grl.unlist(grl1), retain=50))[1], 3095693983)
expect_equal(dim(rearrange(grl.unlist(grl1), retain=50))[2], 3091997226)
## filter.tel = TRUE
expect_equal(dim(rearrange(grl.unlist(grl1), filter.tel = TRUE))[1], 3095693983)
expect_equal(dim(rearrange(grl.unlist(grl1), filter.tel = TRUE))[2], 3091997226)
})
test_that('testing bfb() works', {
## stop('w and wd must be positive')
expect_error(bfb(w=-.05))
expect_error(bfb(3), NA) ## check runs
### even setting set.seed(), the dim() varies
expect_true(is(bfb(3), 'gChain'))
})
### utility functions
test_that('testing vec2ir() works', {
expect_equal(width(vec2ir(c(1, 2, 2, 2))[1]), 2)
expect_equal(width(vec2ir(c(1, 2, 2, 2))[2]), 1)
expect_equal(width(vec2ir(c(1, 2, 2, 2))[3]), 1)
})
test_that('testing ir2vec() works', {
gr = GRanges(1, IRanges(c(3,7,13), c(5,9,16)), strand=c('+','-','-'), seqinfo=Seqinfo("1", 25), name=c("A","B","C"))
expect_equal(length(ir2vec(gr)), 10)
expect_equal(ir2vec(gr)[1], 3)
expect_equal(ir2vec(gr)[10], 16)
expect_equal(length(ir2vec(i2, each=c(2, 4, 6))), 120)
})
test_that('testing gCat() works', {
expect_true(is(gCat(), 'gChain'))
expect_true(is(gCat(gCat(), gCat()), 'gChain'))
foo1 = gChain(grl.unlist(grl1), grl.unlist(grl2)[1:500])
foo2 = gChain(example_dnase[1:200])
expect_true(is(gCat(foo1, foo2), 'gChain'))
})
test_that('testing gUnique() works', {
expect_true(is(gUnique(gChain()), 'gChain'))
})
test_that('testing squeeze() works', {
gr = GRanges(1, IRanges(c(3,7,13), c(5,9,16)), strand=c('+','-','-'), seqinfo=Seqinfo("1", 25), name=c("A","B","C"))
expect_error(squeeze(gr))
ir1 = IRanges(c(3,7,13), c(5,9,16))
expect_equal(width(squeeze(ir1))[1], 3)
expect_equal(width(squeeze(ir1))[3], 4)
expect_equal(squeeze(IRanges()), IRanges())
irlength1 = IRanges(c(1300), c(1600))
expect_equal(as.data.frame(squeeze(irlength1))$width, 301)
})
### grl.split()
test_that('grl.split() works', {
expect_true(is(grl.split(grl2), 'GRangesList'))
expect_equal(length(grl.split(grl2)), 497)
})
## levapply()
test_that('levapply() works', {
gr = GRanges(1, IRanges(c(3,7,13), c(5,9,16)), strand=c('+','-','-'), seqinfo=Seqinfo("1", 25), name=c("A","B","C"))
foo = levapply(width(gr), as.character(seqnames(gr)), function(x) if (length(x)>1) cumsum(c(0, x[1:(length(x)-1)])) else return(0))
expect_equal(foo, c(0, 3, 6))
})
## seqinfo2gr()
test_that('seqinfo2gr() works', {
gr = GRanges(1, IRanges(c(3,7,13), c(5,9,16)), strand=c('+','-','-'), seqinfo=Seqinfo("1", 25), name=c("A","B","C"))
expect_equal(width(seqinfo2gr(gr)), 25)
expect_equal(length(seqinfo2gr(si)), 25)
expect_equal(length(seqinfo2gr(si, strip.empty=TRUE)), 25)
})
## dedup()
test_that('dedup() works', {
expect_equal(dedup(c(rep(2, 10.5), rep(3, 20)))[30], "3.20")
})
## gr.pad()
test_that('gr.pad() works', {
expect_equal(width(gr.pad(gr2, 10)[1]), 16)
expect_equal(width(gr.pad(gr2, 10)[2]), 24)
})
## gr.refactor()
test_that('gr.refactor() works', {
expect_equal(as.character(seqnames(gr.refactor(gr2, sn = c('2', '2'))))[1], '2')
expect_equal(as.character(seqnames(gr.refactor(gr2, sn = c('chr2', '2'))))[1], 'chr2')
expect_equal(as.character(seqnames(gr.refactor(gr2, sn = c('chr2', 'foo'))))[2], 'foo')
## if (is.factor(sn)){
expect_equal(as.character(seqnames(gr.refactor(gr2, sn = factor(c('2', '2')))))[1], '2')
expect_equal(as.character(seqnames(gr.refactor(gr2, sn = factor(c('chr2', '2')))))[1], 'chr2')
expect_equal(as.character(seqnames(gr.refactor(gr2, sn = factor(c('chr2', 'foo')))))[2], 'foo')
})
## gr.tostring()
test_that('gr.tostring() works', {
expect_true(is(gr.tostring(gr2), 'character'))
})
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