inst/unitTests/test_ScoreMatrixBin.R

In genomation: Summary, annotation and visualization of genomic data

# ---------------------------------------------------------------------------- #
# test for ScoreMatrix function
test_ScoreMatrixBin_RleList_GRanges = function()
{
  
  # -----------------------------------------------#
  # usage
  # input RleList
  rl = RleList(chr1 = Rle(rep(c(1,2,3), each=4)), chr2=Rle(rep(c(4,5,6), each=4)))
  
  #1. test for proper workings
  gr1 = GRanges(rep(c('chr1','chr2'), each=2), IRanges(c(1,6,1,6),c(4,9,4,9)), 
                strand=c('+','-','+','-'))
  m1 = matrix(c(1,1,1,1,2,2,2,3,4,4,4,4,5,5,5,6), ncol=4, byrow=T)
  m1 = as(cbind(rowMeans(m1[,1:2]), rowMeans(m1[,3:4])),'ScoreMatrix')
  rownames(m1) = 1:4
  s1 = ScoreMatrixBin(rl, gr1, bin.num=2)
  checkEquals(s1, m1)
  
  #1.1 check for name dropping
  s1.1 = ScoreMatrixBin(rl, gr1, bin.num=1)
  checkEquals(rownames(s1.1),as.character(1:4))
  
  
  #2. test for different bin.op
  for(fun in c('min', 'max', 'median')){
    message('testing:', fun)
    m2 = matrix(c(1,1,1,1,2,2,2,3,4,4,4,4,5,5,5,6), ncol=4, byrow=T)
    m2 = as(cbind(apply(m2[,1:2],1,match.fun(fun)), 
                  apply(m2[,3:4],1,match.fun(fun))),'ScoreMatrix')
    rownames(m2) = 1:4
    s2 = ScoreMatrixBin(rl, gr1, bin.num=2, bin.op=fun)
    checkEquals(s2, m2)  
  }
  
  #3. test strand aware
  m3 = matrix(c(1,1,1,1,2,2,2,3,4,4,4,4,5,5,5,6), ncol=4, byrow=T)
  m3 = as(cbind(rowMeans(m3[,1:2]), rowMeans(m3[,3:4])),'ScoreMatrix')
  rownames(m3) = 1:4
  m3[c(2,4),] = m3[c(2,4),2:1]
  s3 = ScoreMatrixBin(rl, gr1, bin.num=2, strand.aware=T)
  checkEquals(s3, m3)
  
  #4.A bin.num > 1 and dropping chromosomes
  t4 = GRanges(rep(c('chr1','chr2'), times=c(3,2)), IRanges(c(seq(1,20,4)), width=3))
  t4$score = 1
  w4 = GRanges(rep(c('chr3','chr2'), each=2), IRanges(rep(c(13,17), times=2), width=3))
  s4 = suppressWarnings(ScoreMatrixBin(t4, w4, bin.num = 2,type = "bigWig"))
  checkEquals(as.numeric(rownames(as.data.frame(s4))), c(3,4))
  
  #4.B bin.num = 1 and dropping chromosomes
  t5 = GRanges(rep(c('chr1','chr2'), times=c(3,2)), IRanges(c(seq(1,20,4)), width=3))
  t5$score = 1
  w5 = GRanges(rep(c('chr3','chr2'), each=2), IRanges(rep(c(13,17), times=2), width=3))
  s5 = suppressWarnings(ScoreMatrixBin(t5, w5,bin.num = 1,type = "bigWig"))
  checkEquals(as.numeric(rownames(as.data.frame(s5))), c(3,4))
  
  # -----------------------------------------------#
  # errors
  # error for removing all bins
  checkException(SCoreMatrixBin(rl, gr1, bin.num=2), silent=TRUE)
  
  #gr5 = GRanges(rep(c('chr1','chr2'), each=2), IRanges(c(1,5,1,5),c(5,6,5,6)), 
  #              strand=c('+','-','+','-'))
  #checkException(ScoreMatrixBin(rl, gr5, bin.num=3), silent=FALSE) 
}

# ---------------------------------------------------------------------------- #
test_ScoreMatrixBin_GRanges_GRanges = function()
{
  target = GRanges(rep(c(1,2),each=6), 
                   IRanges(rep(c(1,2,3,7,8,9), times=2), width=5),
                   weight = rep(c(1,2),each=6))
  windows = GRanges(rep(c(1,2),each=2), IRanges(rep(c(1,2), times=2), width=5), 
                    strand=c('-','+','-','+'))
  
  # -----------------------------------------------#
  # usage
  # normal function works
  s1 = ScoreMatrixBin(target=target, windows=windows, bin.num=2)
  m1 = matrix(rep(c(1,2,3,3,3,2,3,3,3,2),times=2), ncol=5, byrow=T)
  m1 = as(cbind(rowMeans(m1[,1:3]), rowMeans(m1[,4:5])), 'ScoreMatrix')
  rownames(m1) = 1:4
  checkEquals(s1,m1)
  
  # function with weight col works
  s2 = ScoreMatrixBin(target=target, windows=windows,bin.num=2, weight.col='weight')
  m2 = matrix(rep(c(1,2,3,3,3,2,3,3,3,2),times=2), ncol=5, byrow=T)
  m2[3:4,] = m2[3:4,]*2
  m2 = as(cbind(rowMeans(m2[,1:3]), rowMeans(m2[,4:5])), 'ScoreMatrix')
  rownames(m2) = 1:4
  checkEquals(s2,m2)  
  
  #strand aware
  s3 = ScoreMatrixBin(target=target, windows=windows, bin.num=2, strand.aware=T)
  m3 = matrix(rep(c(1,2,3,3,3,2,3,3,3,2),times=2), ncol=5, byrow=T)
  rownames(m3) = 1:4
  m3 = cbind(rowMeans(m3[,1:3]), rowMeans(m3[,4:5]))
  m3[c(1,3),] = rev(m3[c(1,3),])
  m3 = as(m3, 'ScoreMatrix')
  rownames(m3) = 1:4
  checkEquals(s3,m3)
  
  # -----------------------------------------------#
  # errors
  checkException(ScoreMatrixBin(target, windows, weight.col=''), silent=TRUE)
  
  # number of bins > ncol 
  #expect_warning(ScoreMatrixBin(target, windows, strand.aware = FALSE, bin.num=10))
               
}


# ---------------------------------------------------------------------------- #
test_ScoreMatrixBin_character_GRanges = function()
{
  target = GRanges(rep(c(1,2),each=7), 
                   IRanges(rep(c(1,1,2,3,7,8,9), times=2), width=5),
                   weight = rep(c(1,2),each=7), 
                   strand=c('-', '-', '-', '-', '+', '-', '+', '-', '-', '-', '-', '-', '-', '+'))
  windows = GRanges(rep(c(1,2),each=2), IRanges(rep(c(1,2), times=2), width=5), 
                    strand=c('-','+','-','+'))
  target.paired.end = GRanges(rep(1,each=7), 
                              IRanges(c(1,1,2,3,7,8,9), width=c(19, 19, 19, 19, 16, 16, 16)),
                              strand=rep("+", times=7))
  windows.paired.end = GRanges(rep(c(1),each=4), IRanges(c(7,8,20, 21), width=10), 
                               strand=c('+','+','+','+'))
  # -----------------------------------------------#
  # usage
  # bam file
  bam.file = system.file('unitTests/test.bam', package='genomation')
  s1 = ScoreMatrixBin(bam.file, windows, type='bam', bin.num=2)
  m1 = ScoreMatrixBin(target, windows, bin.num=2)
  checkEquals(s1,m1)
  
  # bam file, rpm=TRUE
  s2 = ScoreMatrixBin(bam.file, windows,bin.num=2, type='bam', rpm=TRUE)
  tot = 1e6/sum(idxstatsBam(normalizePath(bam.file))$mapped)
  m2 = m1*tot
  checkEquals(s2, m2)
  
  #bam file, rpm=FALSE, unique=TRUE
  s3 = ScoreMatrixBin(bam.file, windows,bin.num=2, type='bam', unique=T)
  m3 = ScoreMatrixBin(unique(target), windows, bin.num=2)
  checkEquals(s3,m3)
  
  #bam file, rpm=FALSE, unique=TRUE, extend=1
  s4 = ScoreMatrixBin(bam.file, windows, type='bam', bin.num=2, unique=T, extend=1)
  m4 = ScoreMatrixBin(resize(unique(target), width=1), windows, bin.num=2)
  checkEquals(s4,m4)
  
  # bam file with paired-end reads, rpm=FALSE, unique=TRUE, extend=16
  bam.pe.file = system.file('unitTests/test_pairedend.bam', package='genomation')
  s5 = ScoreMatrixBin(bam.pe.file, windows.paired.end, type='bam', bam.paired.end=TRUE, unique=TRUE, extend=16)
  m5 = ScoreMatrixBin(resize(unique(target.paired.end), width=16), windows.paired.end)
  checkEquals(s5,m5)
  

  if (.Platform$OS.type == "windows")
       return()
  

  # bigWig file with is.noCovNA=TRUE and weight.col="score"
  test_bw <- system.file("unitTests/test.bw", package = "genomation")
  g = GRanges(seqnames=c("chr2","chr19", "chr19", "chr19"),
              IRanges(start=c(1201, 1501, 2401, 2800), width=6),
              strand='*')
  s1 = ScoreMatrixBin(test_bw, g, strand.aware=FALSE, 
                   weight.col="score",is.noCovNA=TRUE,
                   type="bigWig", bin.num=2)
  m1 = matrix(c(rep(0, 2), rep(0.25,2), rep(1,2), rep(NA,2)), 
              nrow=4,  byrow = TRUE)
  rownames(m1) = 1:4
  m1 = as(m1, 'ScoreMatrix')
  checkEquals(s1, m1)
  
  # -----------------------------------------------#
  # errors
  # error upon not specifying the file
  checkException(ScoreMatrixBin('',windows), silent=TRUE)
}

# ---------------------------------------------------------------------------- #
test_that_ScoreMatrix_character_GRange_bigWig = function()
{
  if (.Platform$OS.type == "windows")
    return()
  
  test_bw <- system.file("unitTests/test.bw", package = "genomation")
  
  st = seq(200, 300, 20)
  g = GRanges(rep('chr2', length(st)), IRanges(st, width=5))
  s = ScoreMatrixBin(test_bw, g, type='bigWig', bin.num=2)
  
  m = matrix(-1, ncol=2, nrow=6)
  m[6,1] = -0.833333333333
  m[6,2] = -0.75
  rownames(m) = 1:6
  m = as(m, 'ScoreMatrix')
  checkEquals(s, m)
}

# # ---------------------------------------------------------------------------- #
# test for ScoreMatrixBin function
test_ScoreMatrixBin_RleList_GRangesList = function()
{
  # usage
  # target RleList, windows GRangesList
  target = RleList('c1'= Rle(c(1,1,1,2,2,2,3,3,3)),
                   'c2'= Rle(c(10,10,10,20,20,20,30,30,30)),
                   'c3'= Rle(c(1,2,3,4,5,6,7,8,9)))
  
  gr1 = GRanges(rep('c1',each=3), IRanges(c(1, 4, 7),width=3), strand="-")
  gr2 = GRanges(rep('c2',each=3), IRanges(c(1, 4, 7),width=3), strand="+")
  gr3 = GRanges(rep('c3',each=3), IRanges(c(1, 4, 7),width=3), strand="-")
  grl = GRangesList("transcript1" = gr1, "transcript2" = gr2, 'tr3'=gr3)
  
  s6 = ScoreMatrixBin(target, grl, bin.num=3)
  m6 = matrix(c(1,2,3,10,20,30,2,5,8), ncol=3, byrow=T)
  checkEquals(s6, as(m6, 'ScoreMatrix'))
  
  #2. test for different bin.op
  s7 = ScoreMatrixBin(target, grl, bin.num=1, bin.op='min')
  m7 = matrix(c(1,10,1), ncol=1, byrow=T)
  checkEquals(s7, as(m7, 'ScoreMatrix'))
  
  s8 = ScoreMatrixBin(target, grl, bin.num=1, bin.op='max')
  m8 = matrix(c(3,30,9), ncol=1, byrow=T)
  checkEquals(s8, as(m8, 'ScoreMatrix'))
  
  #3. test strand aware
  m9 = matrix(c(3,2,1,10,20,30,8,5,2), ncol=3, byrow=T)
  s9 = ScoreMatrixBin(target, grl, bin.num=3, strand.aware=T)
  checkEquals(s9, as(m9, "ScoreMatrix"))
  
  #4. test bin.num exception
  checkException(ScoreMatrixBin(target, grl, bin.num=10, strand.aware=T),
                 'Please remove transcripts that are shorter than bin.num',
                 silent=TRUE)

}

# # ---------------------------------------------------------------------------- #
# test for ScoreMatrixBin function
test_ScoreMatrixBin_GRanges_GRangesList = function()
{
  target = RleList('c1'= Rle(c(1,1,1,2,2,2,3,3,3)),
                   'c2'= Rle(c(10,10,10,20,20,20,30,30,30)))
  target = as(target, 'GRanges')
  
  gr1 = GRanges(rep('c1',each=3), IRanges(c(1, 4, 7),width=3), strand="-")
  gr2 = GRanges(rep('c2',each=3), IRanges(c(1, 4, 7),width=3), strand="+")
  grl = GRangesList("transcript1" = gr1, "transcript2" = gr2)
  
  s11 = ScoreMatrixBin(target, grl, bin.num=3, weight.col='score')
  m11 = matrix(c(1,2,3,10,20,30), ncol=3, byrow=T)
  checkEquals(s11, as(m11, 'ScoreMatrix'))
}

# # ---------------------------------------------------------------------------- #
# test for ScoreMatrixBin function
test_ScoreMatrixBin_character_GRangesList = function()
{
  require(GenomicAlignments)
  bam.file = system.file('unitTests/test.bam', package='genomation')
  ga = as(readGAlignments(bam.file),'GRanges')
  
  gr1 = GRanges(rep('1',each=3), IRanges(c(1, 4, 7),width=3), strand="-")
  gr2 = GRanges(rep('2',each=3), IRanges(c(1, 4, 7),width=3), strand="+")
  grl = GRangesList("transcript1" = gr1, "transcript2" = gr2)
  
  m12 = ScoreMatrixBin(ga, grl, bin.num=3)
  s12 = ScoreMatrixBin(bam.file, grl, type='bam', bin.num=3)
  
  checkEquals(s12, as(m12, "ScoreMatrix"))
}