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.


Reference manual

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1.0 by Ahmed Alhendi, 2 years ago

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Authors: Ahmed Alhendi [aut, cre]

Documentation:   PDF Manual  

GPL-3 license

Depends on ComplexHeatmap, circlize, stats

See at CRAN