Nothing
#!/usr/bin/env Rscript
exampleData <- system.file("exampleData", package="PeakError")
arg.vec <- file.path(exampleData, c("peaks.bed", "labels.bed"))
arg.vec <- commandArgs(trailingOnly=TRUE)
if(length(arg.vec) != 2){
stop("Usage: compute_error.R peaks.bed labels.bed > errors.bed")
}
peaks.bed <- arg.vec[1]
labels.bed <- arg.vec[2]
peak.classes <- c(
chrom="character",
chromStart="integer",
chromEnd="integer")
peaks <- read.table(
peaks.bed,
colClasses=peak.classes,
col.names=names(peak.classes))
message("read ", nrow(peaks), " peaks")
labels.classes <- c(
chrom="character",
chromStart="integer",
chromEnd="integer",
annotation="character")
labels <- read.table(
labels.bed,
colClasses=labels.classes,
col.names=names(labels.classes))
message("read ", nrow(labels), " labels")
if(!require(PeakError)){
if(!require(devtools)){
install.packages("devtools")
library(devtools)
}
install_github("tdhock/PeakError")
library(PeakError)
}
errors <- PeakError(peaks, labels)
write.table(errors, sep="\t", quote=FALSE, row.names=FALSE)
message("computed errors for ", nrow(errors), " labels")
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