mirnaCovar: Adding covariates and batch information to miRNAseq raw...

In kendomaniac/docker4seq: Running NGS computing demanding applications, e.g reads mapping and counting, wrapped in docker containers

Adding covariates and batch information to miRNAseq raw counts output

Description

This function modifies the all.counts.txt table generated from miRNAseq adding covariates and batch information

Usage

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(s)

Raffaele Calogero

Examples

## Not run: 
   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())

## End(Not run)

kendomaniac/docker4seq documentation built on Sept. 3, 2024, 6:42 p.m.