fcount_meantransform: Transform a featurecount output to a data frame of...

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

Description

Transform a featurecount output to a data frame of library-normalized mean counts

Usage

fcount_meantransform(fcountOutput, samplenames, filterByCount = NULL,
  boxplot = TRUE)

Arguments

fcountOutput	Featurecount output in a data frame
samplenames	The name of samples (exclusing replicate ID etc). Replicates of the samples will be grouped together for calculating mean..
filterByCount	A value, if given it will first filter genes by raw mean expression <= given threshold.
boxplot	Logical. Draw a boxplot or normalized counts?

Value

A data frame of library-normalized mean counts

Examples

fc <- system.file("extdata", "fcount_mouse.tsv", package="vivlib")
fout <- read.delim(fc)
samples <- c(paste0("cont_", 1:3), paste0("KD_",1:3))
out <- fcount_meantransform(fcountOutput = fout, samplenames = samples, filterByCount = 1000, boxplot = TRUE)

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