countToFPKM: Convert Counts to Fragments per Kilobase of Transcript per Million (FPKM)

Implements the algorithm described in Trapnell,C. et al. (2010) <doi: 10.1038/nbt.1621>. This function takes read counts matrix of RNA-Seq data, feature lengths which can be retrieved using 'biomaRt' package, and the mean fragment lengths which can be calculated using the 'CollectInsertSizeMetrics(Picard)' tool. It then returns a matrix of FPKM normalised data by library size and feature effective length. It also provides the user with a quick and reliable function to generate FPKM heatmap plot of the highly variable features in RNA-Seq dataset.

Getting started

Package details

AuthorAhmed Alhendi [aut, cre]
MaintainerAhmed Alhendi <[email protected]>
LicenseGPL-3
Version1.0
URL https://github.com/AAlhendi1707/countToFPKM
Package repositoryView on CRAN
Installation Install the latest version of this package by entering the following in R:
install.packages("countToFPKM")

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countToFPKM documentation built on May 1, 2019, 8:06 p.m.