mirnaCovar.Rd
This function modifies the all.counts.txt table generated from miRNAseq adding covariates and batch information
mirnaCovar(experiment.folder, covariates = NULL, batches = NULL, output.folder)
experiment.folder, | a character string indicating the full paths to miRNAseq input file, i.e. including the name of the file |
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covariates, | a character vector indicating the covariates associated to each sample, e.g. c("Cov.1", "Cov.1", "Cov.1", "Cov.1", "Cov.2", "Cov.2", "Cov.2", "Cov.2"). Covariates are required for differential expression analysis |
batches, | a character vector indicating the covariates associated to each sample, e.g. c("bath.1", "bath.1", "bath.2", "bath.2", "batch.1", "batch.1", "batch.2", "batch.2"). Batch info might be required for differential expression analysis |
output.folder, | a character vector indicating the paths to miRNAseq output folder |
Returns 0 and a count file, i.e. all.counts.txt, with the prefix "w_covar" or w_covar_batch depending if only covariates were added or also batch info were added
if (FALSE) { system("wget 130.192.119.59/public/test.mirna.analysis.zip") unzip("test.mirna.analysis.zip") setwd("test.mirna.analysis") library(docker4seq) mirnaCovar(experiment.folder=paste(getwd(), "all.counts.txt", sep="/"), covariates=c("Cov.1", "Cov.1", "Cov.1", "Cov.1", "Cov.1", "Cov.1", "Cov.2", "Cov.2", "Cov.2", "Cov.2", "Cov.2", "Cov.2"), batches=c("bath.1", "bath.1", "bath.2", "bath.2", "batch.1", "batch.1", "batch.2", "batch.2","batch.1", "batch.1","bath.2", "bath.2"), output.folder=getwd()) }