comparison edgeR_repenrich.R @ 13:530626b0757c draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit df6b9491ad06e8a85e67c663b68db3cce3eb0115

12:89e05f831259

})

options(stringAsFactors = FALSE, useFancyQuotes = FALSE)

# get options, using the spec as defined by the enclosed list.
# we read the options from the default: commandArgs(TRUE).
spec <- matrix(
    c(
        "quiet", "q", 0, "logical",
        "outfile", "o", 1, "character",
        "countsfile", "n", 1, "character",
        "factorName", "N", 1, "character",
        "levelNameA", "A", 1, "character",
        "levelNameB", "B", 1, "character",
        "levelAfiles", "a", 1, "character",
        "levelBfiles", "b", 1, "character",
        "alignmentA", "i", 1, "character",
        "alignmentB", "j", 1, "character",
        "plots", "p", 1, "character"
    ),
    byrow = TRUE, ncol = 4
)
opt <- getopt(spec)

}
for (element in names(listB[-1])) {
    counts <- cbind(counts, listB[[element]][, 4])
}
colnames(counts) <- c(names(listA[-1]), names(listB[-1]))

# build aligned counts vector
filesi <- fromJSON(opt$alignmentA, method = "C", unexpected.escape = "error")
filesj <- fromJSON(opt$alignmentB, method = "C", unexpected.escape = "error")
sizes <- c()
for (file in filesi) {
    sizes <- c(sizes, read.delim(file, header = TRUE)[1, 1])
}
for (file in filesj) {
    sizes <- c(sizes, read.delim(file, header = TRUE)[1, 1])
}

# build a meta data object
meta <- data.frame(
    row.names = colnames(counts),
    condition = c(rep(opt$levelNameA, length(filesA)), rep(opt$levelNameB, length(filesB))),

results <- cbind(TE_item = rownames(results), results)
colnames(results) <- c("TE_item", "log2FC", "FDR", "Class", "Type")
results$log2FC <- format(results$log2FC, digits = 5)
results$FDR <- format(results$FDR, digits = 5)
write.table(results, opt$outfile, quote = FALSE, sep = "\t", col.names = TRUE, row.names = FALSE)

cat("Session information:\n\n")
sessionInfo()

13:530626b0757c

})

options(stringAsFactors = FALSE, useFancyQuotes = FALSE)

# get options, using the spec as defined by the enclosed list.
spec <- matrix(
    c(
        "quiet", "q", 0, "logical",
        "outfile", "o", 1, "character",
        "countsfile", "n", 1, "character",
        "factorName", "N", 1, "character",
        "levelNameA", "A", 1, "character",
        "levelNameB", "B", 1, "character",
        "levelAfiles", "a", 1, "character",
        "levelBfiles", "b", 1, "character",
        "plots", "p", 1, "character"
    ),
    byrow = TRUE, ncol = 4
)
opt <- getopt(spec)

}
for (element in names(listB[-1])) {
    counts <- cbind(counts, listB[[element]][, 4])
}
colnames(counts) <- c(names(listA[-1]), names(listB[-1]))
sizes <- colSums(counts)

# build a meta data object
meta <- data.frame(
    row.names = colnames(counts),
    condition = c(rep(opt$levelNameA, length(filesA)), rep(opt$levelNameB, length(filesB))),

results <- cbind(TE_item = rownames(results), results)
colnames(results) <- c("TE_item", "log2FC", "FDR", "Class", "Type")
results$log2FC <- format(results$log2FC, digits = 5)
results$FDR <- format(results$FDR, digits = 5)
write.table(results, opt$outfile, quote = FALSE, sep = "\t", col.names = TRUE, row.names = FALSE)