comparison deseq2.R @ 41:0a0a3388e3f2 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"

40:ed9e8345a292

  "help", "h", 0, "logical",
  "cores", "s", 0, "integer",
  "batch_factors", "w", 1, "character",
  "outfile", "o", 1, "character",
  "countsfile", "n", 1, "character",
  "rlogfile", "r", 1, "character",
  "vstfile", "v", 1, "character",
  "header", "H", 0, "logical",
  "factors", "f", 1, "character",
  "files_to_labels", "l", 1, "character",

dds <- get_deseq_dataset(sample_table, header = opt$header, design_formula = design_formula, tximport = opt$tximport, txtype = opt$txtype, tx2gene = opt$tx2gene)
# estimate size factors for the chosen method
if (!is.null(opt$esf)) {
    dds <- estimateSizeFactors(dds, type = opt$esf)
}
apply_batch_factors <- function(dds, batch_factors) {
  rownames(batch_factors) <- batch_factors$identifier
  batch_factors <- subset(batch_factors, select = -c(identifier, condition))
  dds_samples <- colnames(dds)
  batch_samples <- rownames(batch_factors)

41:0a0a3388e3f2

  "help", "h", 0, "logical",
  "cores", "s", 0, "integer",
  "batch_factors", "w", 1, "character",
  "outfile", "o", 1, "character",
  "countsfile", "n", 1, "character",
  "sizefactorsfile", "F", 1, "character",
  "rlogfile", "r", 1, "character",
  "vstfile", "v", 1, "character",
  "header", "H", 0, "logical",
  "factors", "f", 1, "character",
  "files_to_labels", "l", 1, "character",

dds <- get_deseq_dataset(sample_table, header = opt$header, design_formula = design_formula, tximport = opt$tximport, txtype = opt$txtype, tx2gene = opt$tx2gene)
# estimate size factors for the chosen method
if (!is.null(opt$esf)) {
    dds <- estimateSizeFactors(dds, type = opt$esf)
}

# estimate size factors for each sample
# - https://support.bioconductor.org/p/97676/
if (!is.null(opt$sizefactorsfile)) {
    nm <- assays(dds)[["avgTxLength"]]
    if (!is.null(nm)) {
        ## Recommended: takes into account tximport data
        cat("\nsize factors for samples: taking tximport data into account\n")
        size_factors <- estimateSizeFactorsForMatrix(counts(dds) / nm)
    } else {
        norm_factors <- normalizationFactors(dds)
        if (!is.null(norm_factors)) {
            ## In practice, gives same results as above.
            cat("\nsize factors for samples: no tximport data, using derived normalization factors\n")
            size_factors <- estimateSizeFactorsForMatrix(norm_factors)
        } else {
            ## If we have no other information, estimate from raw.
            cat("\nsize factors for samples: no tximport data, no normalization factors, estimating from raw data\n")
            size_factors <- estimateSizeFactorsForMatrix(counts(dds))
        }
    }
    write.table(size_factors, file = opt$sizefactorsfile, sep = "\t", col.names = F, quote = FALSE)
}

apply_batch_factors <- function(dds, batch_factors) {
  rownames(batch_factors) <- batch_factors$identifier
  batch_factors <- subset(batch_factors, select = -c(identifier, condition))
  dds_samples <- colnames(dds)
  batch_samples <- rownames(batch_factors)