# NOT RUN {
library(PeakSegDisk)
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))
write.table(
four, tmp <- tempfile(),
sep="\t", row.names=FALSE, col.names=FALSE)
pstr <- "10.5"
PeakSegFPOP_file(tmp, pstr)
outf <- function(suffix){
paste0(tmp, "_penalty=", pstr, "_", suffix)
}
segments.bed <- outf("segments.bed")
first.seg.line <- fread.first(segments.bed, col.name.list$segments)
last.seg.line <- fread.last(segments.bed, col.name.list$segments)
loss.tsv <- outf("loss.tsv")
loss.row <- fread.first(loss.tsv, col.name.list$loss)
seg.bases <- first.seg.line$chromEnd - last.seg.line$chromStart
loss.row$bases == seg.bases
# }
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