countToFPKM (1.0)

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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) . 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.

Maintainer: Ahmed Alhendi
Author(s): Ahmed Alhendi [aut, cre]

License: GPL-3

Uses: circlize

Released 3 months ago.



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