countToFPKM v1.0

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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.

Functions in countToFPKM

Name Description
fpkm countToFPKM Convert counts to Fragments Per Kilobase of transcript per Million mapped reads (FPKM)
fpkmheatmap countToFPKM A FPKM heatmap plot of the highly variable features in RNA-Seq dataset
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Details

Date 2019-03-22
License GPL-3
URL https://github.com/AAlhendi1707/countToFPKM
BugReports https://github.com/AAlhendi1707/countToFPKM/issues
NeedsCompilation no
Packaged 2019-04-07 16:59:02 UTC; asna4
Repository CRAN
Date/Publication 2019-04-07 17:42:43 UTC

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