# 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)
read.table(
tmp, col.names=col.name.list$coverage)
pstr <- "10.5"
PeakSegFPOP_file(tmp, pstr)
outf <- function(suffix){
paste0(tmp, "_penalty=", pstr, "_", suffix)
}
fread.first(outf("segments.bed"), col.name.list$segments)
fread.first(outf("loss.tsv"), col.name.list$loss)
# }
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