# NOT RUN {
r <- function(chrom, chromStart, chromEnd, coverage){
data.frame(chrom, chromStart, chromEnd, coverage)
}
four <- rbind(
r("chr1", 0, 10, 2),
r("chr1", 10, 20, 10),
r("chr1", 20, 30, 14),
r("chr1", 30, 40, 13))
dir.create(prob.dir <- tempfile())
coverage.bedGraph <- file.path(prob.dir, "coverage.bedGraph")
write.table(
four, coverage.bedGraph,
sep="\t", row.names=FALSE, col.names=FALSE)
pstr <- "10.5"
result.list <- PeakSegDisk::PeakSegFPOP_file(coverage.bedGraph, pstr)
dir(prob.dir)
## segments file can be read to see optimal segment means.
outf <- function(suffix){
paste0(coverage.bedGraph, "_penalty=", pstr, suffix)
}
segments.bed <- outf("_segments.bed")
seg.df <- read.table(segments.bed)
names(seg.df) <- col.name.list$segments
seg.df
## loss file can be read to see optimal Poisson loss, etc.
loss.tsv <- outf("_loss.tsv")
loss.df <- read.table(loss.tsv)
names(loss.df) <- col.name.list$loss
loss.df
# }
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