Adding covariates and batch information to miRNAseq raw counts output

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)

Arguments

experiment.folder,

a character string indicating the full paths to miRNAseq input file, i.e. including the name of the file

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

Value

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

Author

Raffaele Calogero

Examples

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())
}