makeVoomInput: Make Voom transformed input for BarCodePlot and ROAST test

In vivekbhr/vivlib: An R package for useful bioinformatics wrappers

Description

Make Voom transformed input for BarCodePlot and ROAST test

Usage

makeVoomInput(fcountOutput, design, genome = "mm10", plotFile = NULL)

Arguments

fcountOutput	A featurecounts output file
design	A data frame containing design information. rownames should correspond to columns in count file and column could be control/test or any set of factors.
genome	Genome of organism to fetch annotation (available : "mm10", "hg38" , "dm6")
plotFile	File name to output filtering plots (.pdf).

Value

A plot (as pdf) and a voom transformed output as list.

Examples

fc <- system.file("extdata", "fcount_mouse.tsv", package="vivlib")
design <- data.frame(row.names = c(paste0("cnt_", 1:3), paste0("KD_",1:3)),
                     condition = rep(c("cnt","KD"), each = 3) )
makeVoomInput(fcountOutput = fc, design = design, plotFile = "test.pdf")

vivekbhr/vivlib documentation built on May 3, 2019, 6:13 p.m.