tests/testthat/test-getTagMatrix.R

In YuLab-SMU/ChIPseeker: ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

library(ChIPseeker)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)

context("test getTagMatrix() and related functions")

test_that("getBioRegion function", {
  
  # test three kinds of regions derived from getBioRegion()
  txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
  
  gene_start <- getBioRegion(TxDb = txdb,
                             upstream = 1000,
                             downstream = 1000,
                             by = 'gene',
                             type = "start_site")
  expect_is(gene_start,"GRanges")
  
  gene_end <- getBioRegion(TxDb = txdb,
                           upstream = 1000,
                           downstream = 1000,
                           by = 'gene',
                           type = "end_site")
  expect_is(gene_end,"GRanges")
  
  gene_body <- getBioRegion(TxDb = txdb,
                            upstream = 1000,
                            downstream = 1000,
                            by = 'gene',
                            type = "body")
  expect_is(gene_body,"GRanges")
  
  })

test_that("getPromoters functions",{
  
  # test two kinds of regions derived from getPromoters
  txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
  
  gene <- getPromoters(TxDb=txdb,
                       upstream=1000,
                       downstream=1000,
                       by = "gene")
  
  transcript <- getPromoters(TxDb=txdb,
                             upstream=1000,
                             downstream=1000,
                             by = "transcript")
  
  expect_is(gene,"GRanges")
  expect_is(transcript,"GRanges")
  
})

test_that("makeBioRegionFromGranges function",{
  
  # we consider transcript region as enhancer region
  # and make self-made granges object
  # they can be the same in the form of granges object
  txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
  enhancer <- transcripts(txdb)[1:5000,]
  
  ## we test three kinds of region, start_site, end_site and body
  enhancer_body <- makeBioRegionFromGranges(gr = enhancer,
                                            by = "enhancer",
                                            type = "body")
  
  enhancer_start <- makeBioRegionFromGranges(gr = enhancer,
                                             by = "enhancer",
                                             type = "start_site",
                                             upstream = 1000,
                                             downstream = 1000)
  
  enhancer_end <- makeBioRegionFromGranges(gr = enhancer,
                                           by = "enhancer",
                                           type = "end_site",
                                           upstream = 1000,
                                           downstream = 1000)
  
  expect_is(enhancer_body,"GRanges")
  expect_is(enhancer_start,"GRanges")
  expect_is(enhancer_end,"GRanges")
  
  ## test the label
  expect_equal(attr(enhancer_body,'label'),c("enhancer_SS","enhancer_TS"))
  expect_equal(attr(enhancer_start,'label'),"enhancer_SS")
  expect_equal(attr(enhancer_end,'label'),"enhancer_TS")
  
})

test_that("getTagMatrix function for single peak file",{
  
  peak <- getSampleFiles()[[4]]
  txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
  
  # make the window by getBioRegion()
  gene_start <- getBioRegion(TxDb = txdb,
                             upstream = 1000,
                             downstream = 1000,
                             by = 'gene',
                             type = "start_site")
  
  # make the window by makeBioRegionFromGranges()
  enhancer <- transcripts(txdb)[1:5000,]
  
  enhancer_body <- makeBioRegionFromGranges(gr = enhancer,
                                            by = "enhancer",
                                            type = "body")
  
  # test input window parameter
  mt1 <- getTagMatrix(peak = peak,
                      windows = gene_start,
                      weightCol = "V5")
  
  expect_is(mt1, "matrix")
  
  # without extending flank
  mt2_1 <- getTagMatrix(peak = peak,
                        windows = enhancer_body,
                        weightCol = "V5",
                        nbin = 800)
  
  expect_is(mt2_1, "matrix")
  
  # extend flank by rel object
  mt2_2 <- getTagMatrix(peak = peak,
                        windows = enhancer_body,
                        weightCol = "V5",
                        upstream = rel(0.2),
                        downstream = rel(0.2),
                        nbin = 800)
  
  expect_is(mt2_2, "matrix")
  
  # extend flank by actual number
  mt2_3 <- getTagMatrix(peak = peak,
                        windows = enhancer_body,
                        weightCol = "V5",
                        upstream = 1000,
                        downstream = 1000,
                        nbin = 800)
  
  expect_is(mt2_3, "matrix")
  
  # test input without window parameter 
  
  # make window through txdb object
  mt3 <- getTagMatrix(peak = peak,
                      weightCol = "V5",
                      TxDb = txdb,
                      by = "gene",
                      type = "start_site",
                      upstream = 3000,
                      downstream = 3000)
  
  expect_is(mt3, "matrix")
  
  # make window through self-made grange object
  mt4 <- getTagMatrix(peak = peak,
                      weightCol = "V5",
                      TxDb = enhancer,
                      by = "gene",
                      type = "start_site",
                      upstream = 1000,
                      downstream = 1000)
  
  expect_is(mt4, "matrix")
  
  # without extending flank
  mt5_1 <- getTagMatrix(peak = peak,
                        weightCol = "V5",
                        TxDb = txdb,
                        by = "gene",
                        type = "body",
                        nbin = 800)
  
  expect_is(mt5_1, "matrix")
  
  # extend flank by rel object
  mt5_2 <- getTagMatrix(peak = peak,
                        TxDb = enhancer,
                        weightCol = "V5",
                        by = "enhancer",
                        type = "body",
                        upstream = rel(0.2),
                        downstream = rel(0.2),
                        nbin = 800)
  
  expect_is(mt5_2, "matrix")
  
  # extend flank by actual number
  mt5_3 <- getTagMatrix(peak = peak,
                        TxDb = txdb,
                        weightCol = "V5",
                        by = "gene",
                        type = "body",
                        upstream = 1000,
                        downstream = 1000,
                        nbin = 800)
  
  expect_is(mt5_3, "matrix")
  
})