count2FPKM: Converting gene expression data from raw count to FPKM

In reese3928/RNAAgeCalc: A multi-tissue transcriptional age calculator

Description

This function converts gene expression data from raw count to FPKM by using getRPKM

Usage

count2FPKM(rawcount, genelength = NULL, idtype = "SYMBOL")

Arguments

rawcount	a matrix or data frame which contains gene expression counts data.
genelength	gene length in bp. The size of 'genelength' should be equal to the number of rows in 'rawcount'. This argument is optional. If not provided, gene length is obtained from the internal database.
idtype	a string which indicates the gene id type in rawcount matrix. It should be one of "SYMBOL", "ENSEMBL", "ENTREZID" or "REFSEQ". Default is "SYMBOL".

Value

a data frame contains FPKM.

References

Carlson M (2019). org.Hs.eg.db: Genome wide annotation for Human. R package version 3.8.2.

Collado-Torres, Leonardo, et al. "Reproducible RNA-seq analysis using recount2." Nature biotechnology 35.4 (2017): 319-321.

Examples

data(countExample)
head(rawcount)
fpkm = count2FPKM(rawcount)
head(fpkm)

reese3928/RNAAgeCalc documentation built on Sept. 25, 2020, 1:01 a.m.