Count To FPKM Manual
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Package ‘countToFPKM’
March 22, 2019
Type Package
Title Convert counts to Fragments Per Kilobase of transcript per
Million (FPKM).
Version 1.0
Date 2019-03-22
Author Ahmed Alhendi (Dr.)
Maintainer Ahmed Alhendi <asna4@le.ac.uk>
Description Convert a numeric matrix of features (rows) and conditions (columns) with raw fea-
ture counts of RNA-seq data to fragments per kilobase of transcript per million mapped reads.
License GNU General Public License v3.0
Rtopics documented:
countToFPKM-package................................... 1
Index 3
countToFPKM-package
Convert counts to Fragments Per Kilobase of transcript per Million
(FPKM).
Description
Convert a numeric matrix of features (rows) and conditions (columns) with raw feature counts of
RNA-seq data to fragments per kilobase of transcript per million mapped reads.
Details
The DESCRIPTION file: This package was not yet installed at build time.
This package is to convert a numeric matrix of features (rows) and conditions (columns) with raw
feature counts of RNA-seq data to fragments per kilobase of transcript per million mapped reads.
@param counts A numeric matrix of raw feature counts i.e. fragments assigned to each gene.
@param featureLength A numeric vector with feature lengths. @param meanFragmentLength A
numeric vector with mean fragment lengths. @return fpkm A numeric matrix normalized by library
size and feature length.
1
2countToFPKM-package
Author(s)
Ahmed Alhendi (Dr.) Maintainer: Ahmed Alhendi <asna4@le.ac.uk>
References
Trapnell,C. et al. (2010) Transcript assembly and quantification by RNA-seq reveals unannotated
transcripts and isoform switching during cell differentiation. Nat. Biotechnol., 28, 511–515. doi:
10.1038/nbt.1621
Lior Pachter. Models for transcript quantification from RNA-Seq. arXiv:1104.3889v2
Examples
foo <- countToFpkm (counts, featureLength, meanFragmentLength)
