fpkmFromCounts: Calculate FPKM.

In traversc/trqwe: Performance oriented statistical metrics and utility functions.

Description

Calculates FPKM from a count matrix.

Usage

fpkmFromCounts(mat, gene_lengths, uq_norm = T)

Arguments

mat	An integer matrix representing the counts of a RNA-Seq dataset.
gene_lengths	A named vector with the length of each gene.
uq_norm	If TRUE, will perform upper-quartile normalization.

Value

A matrix containing FPKM with the same dimensions as mat.

See Also

FPKM-UQ - A normalized read count in which gene expression values, in FPKM, are divided by the 75th percentile value.

https://gdc-docs.nci.nih.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/

http://vinaykmittal.blogspot.com/2013/10/fpkmrpkm-normalization-caveat-and-upper.html

traversc/trqwe documentation built on Dec. 4, 2020, 4:21 a.m.