counts2fpkm: Fragments per kilobase per million

In Tmisc: Turner Miscellaneous

Fragments per kilobase per million

Description

Takes a count matrix and a vector of gene lengths and returns an optionally log2-transformed FPKM matrix. Modified from edgeR.

Usage

counts2fpkm(x, length, log = FALSE, prior.count = 0.25)

Arguments

x	a matrix of counts
length	a vector of length nrow(x) giving length in bases
log	logical, if TRUE, then log2 values are returned.
prior.count	average count to be added to each observation to avoid taking log of zero. Used only if log=TRUE.

Value

A matrix of FPKM values.

Examples

## Not run: 
library(readr)
library(dplyr)
countdata <- read_csv("http://files.figshare.com/2439061/GSE37704_featurecounts.csv") 
counts <- countdata %>% select(countdata, starts_with("SRR")) %>% as.matrix
counts2fpkm(counts, countdata$length)

## End(Not run)
  

Tmisc documentation built on Aug. 23, 2023, 1:07 a.m.