Mercurial > repos > artbio > gsc_scran_normalize
diff scran-normalize.R @ 2:6864acb21714 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize commit a14fb3d106b647c4f1dea2c8d3ac7c1e8848b21c
author | artbio |
---|---|
date | Sun, 10 Dec 2023 00:27:45 +0000 |
parents | fb2f1b8b0013 |
children | cc768b0f41cf |
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--- a/scran-normalize.R Sun Dec 04 01:01:01 2022 +0000 +++ b/scran-normalize.R Sun Dec 10 00:27:45 2023 +0000 @@ -1,15 +1,15 @@ -# load packages that are provided in the conda env options(show.error.messages = FALSE, error = function() { cat(geterrmessage(), file = stderr()) q("no", 1, FALSE) - } + } ) loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") warnings() library(optparse) library(scran) +library(dynamicTreeCut) # Arguments option_list <- list( @@ -20,12 +20,6 @@ help = "Input file that contains count values to transform" ), make_option( - c("-s", "--sep"), - default = "\t", - type = "character", - help = "File separator [default : '%default' ]" - ), - make_option( "--cluster", default = FALSE, action = "store_true", @@ -53,18 +47,15 @@ ) opt <- parse_args(OptionParser(option_list = option_list), - args = commandArgs(trailingOnly = TRUE)) + args = commandArgs(trailingOnly = TRUE)) -if (opt$sep == "tab") { - opt$sep <- "\t" - } data <- read.table( opt$data, check.names = FALSE, header = TRUE, row.names = 1, - sep = opt$sep + sep = "\t" ) ## Import data as a SingleCellExperiment object @@ -81,7 +72,7 @@ sce <- computeSumFactors(sce) } -sce <- normalize(sce) +sce <- logNormCounts(sce) logcounts <- data.frame(genes = rownames(sce), round(logcounts(sce), digits = 5), check.names = FALSE)