tests/testthat/test-maxRegionGap.R

In derfinder: Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach

library("GenomicRanges")
library("bumphunter")

########### from ?findRegions

## Preprocess the data
prep <- preprocessCoverage(genomeData,
    cutoff = 0, scalefac = 32, chunksize = 1e3,
    colsubset = NULL
)

## Get the F statistics
fstats <- genomeFstats

## Find the regions
regs <- findRegions(prep$position, fstats, "chr21", verbose = TRUE)


#### Scenario:
## Start from a regular GenomicRanges
## Use filterData() and findRegions() to collapse regions

## First, set as a GRanges
gr <- regs

## Filter the data to get positions above a cutoff
filt <- filterData(GenomicRanges::coverage(gr),
    cutoff = 0,
    returnCoverage = TRUE, returnMean = TRUE
)

## Find regions with no maxRegionGap
nogap_derfinder <- findRegions(filt$position, filt$meanCoverage,
    chr = "chr21",
    cutoff = 0
)
nogap_bumphunter <- bumphunter::regionFinder(
    x = as.numeric(filt$meanCoverage),
    chr = rep("chr21", length(filt$meanCoverage)),
    pos = which(filt$position > 0), cutoff = 0, maxGap = 1
)
## order the results
nogap_bumphunter <- nogap_bumphunter[order(nogap_bumphunter$start), ]

## Now with a gap
gap_derfinder <- findRegions(filt$position, filt$meanCoverage,
    chr = "chr21",
    cutoff = 0, maxRegionGap = 50
)
gap_bumphunter <- bumphunter::regionFinder(
    x = as.numeric(filt$meanCoverage),
    chr = rep("chr21", length(filt$meanCoverage)),
    pos = which(filt$position > 0), cutoff = 0, maxGap = 50
)
gap_bumphunter <- gap_bumphunter[order(gap_bumphunter$start), ]

## Remove the excess stuff
remove_derfinder <- function(x) {
    mcols(x) <- mcols(x)[, c("value", "area", "indexStart", "indexEnd")]
    return(x)
}
remove_bumphunter <- function(x) {
    x <- GRanges(x[, -which(colnames(x) %in% c("cluster", "clusterL", "L"))])
    names(x) <- rep("up", length(x))
    return(x)
}

## now check that the regions match (start and ends)
## as well as the rest except for the cluster stuff
test_that("maxRegionGap works", {
    expect_equal(
        remove_derfinder(nogap_derfinder),
        remove_bumphunter(nogap_bumphunter)
    )
    expect_equal(
        remove_derfinder(gap_derfinder),
        remove_bumphunter(gap_bumphunter)
    )
})