comparison deseq2.R @ 31:9a882d108833 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf

30:8fe98f7094de

# setup R error handling to go to stderr
options(show.error.messages = FALSE, error = function() {
  cat(geterrmessage(), file = stderr())
  q("no", 1, FALSE)
})

# we need that to not crash galaxy with an UTF8 error on German LC settings.
loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")

library("getopt")
library("tools")
options(stringAsFactors = FALSE, useFancyQuotes = FALSE)
args <- commandArgs(trailingOnly = TRUE)

  "fit_type", "t", 1, "integer",
  "many_contrasts", "m", 0, "logical",
  "outlier_replace_off", "a", 0, "logical",
  "outlier_filter_off", "b", 0, "logical",
  "auto_mean_filter_off", "c", 0, "logical",
  "beta_prior_off", "d", 0, "logical",
  "alpha_ma", "A", 1, "numeric",
  "prefilter", "P", 0, "logical",
  "prefilter_value", "V", 1, "numeric"
), byrow = TRUE, ncol = 4)
opt <- getopt(spec)

  }
  cat("\n---------------------\n")
}

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"]]

  independent_filtering <- FALSE
  if (verbose) cat("automatic filtering on the mean off\n")
}

# shrinkage of LFCs
if (is.null(opt$beta_prior_off)) {
  beta_prior <- TRUE
} else {
  beta_prior <- FALSE
  if (verbose) cat("beta prior off\n")
}

# dispersion fit type
if (is.null(opt$fit_type)) {
  fit_type <- "parametric"
} else {

31:9a882d108833

# setup R error handling to go to stderr
options(show.error.messages = FALSE, error = function() {
  cat(geterrmessage(), file = stderr())
  q("no", 1, FALSE)
})

library("getopt")
library("tools")
options(stringAsFactors = FALSE, useFancyQuotes = FALSE)
args <- commandArgs(trailingOnly = TRUE)

  "fit_type", "t", 1, "integer",
  "many_contrasts", "m", 0, "logical",
  "outlier_replace_off", "a", 0, "logical",
  "outlier_filter_off", "b", 0, "logical",
  "auto_mean_filter_off", "c", 0, "logical",
  "use_beta_priors", "d", 0, "logical",
  "alpha_ma", "A", 1, "numeric",
  "prefilter", "P", 0, "logical",
  "prefilter_value", "V", 1, "numeric"
), byrow = TRUE, ncol = 4)
opt <- getopt(spec)

  }
  cat("\n---------------------\n")
}

dds <- get_deseq_dataset(sample_table, header = opt$header, design_formula = design_formula, tximport = opt$tximport, txtype = opt$txtype, tx2gene = opt$tx2gene)

# use/estimate size factors with the chosen method
if (!is.null(opt$esf)) {
    if (opt$esf %in% list("ratio", "poscounts", "iterate")) {
        cat("Calculating size factors de novo\n")
        dds <- estimateSizeFactors(dds, type = opt$esf)
    } else {
        sf_table <- read.table(opt$esf)
        # Sort the provided size factors just in case the order differs from the input file order.
        merged_table <- merge(sample_table, sf_table, by.x = 0, by.y = 1, sort = FALSE)
        sf_values <- as.numeric(unlist(merged_table[5]))
        "sizeFactors"(dds) <- sf_values

        cat("Using user-provided size factors:\n")
        print(sf_values)
    }
} else {
    cat("No size factor was used\n")
}


# estimate size factors for each sample
# - https://support.bioconductor.org/p/97676/
if (!is.null(opt$sizefactorsfile)) {
    nm <- assays(dds)[["avgTxLength"]]

  independent_filtering <- FALSE
  if (verbose) cat("automatic filtering on the mean off\n")
}

# shrinkage of LFCs
if (is.null(opt$use_beta_priors)) {
  beta_prior <- FALSE
  if (verbose)
    cat("Applied default - beta prior off\n")
} else {
  beta_prior <- opt$use_beta_priors
}
sprintf("use_beta_prior is set to %s", beta_prior)


# dispersion fit type
if (is.null(opt$fit_type)) {
  fit_type <- "parametric"
} else {