polyester (version 1.6.0)

fpkm_to_counts: Turn FPKMs from a ballgown object into estimated counts for transcripts

Description

Turn FPKMs from a ballgown object into estimated counts for transcripts

Usage

fpkm_to_counts(bg = NULL, mat = NULL, tlengths = NULL, mean_rps = 1e+08, threshold = 0)

Arguments

bg

ballgown object created from real RNA-seq dataset

mat

matrix of isoform-level FPKMs from which to derive counts. Rows should represent transcripts and columns should represent counts. Provide exactly one of bg or mat.

tlengths

if using mat instead of bg, vector of transcript lengths. Entries correspond to the rows of mat. Lengths should only count the nucleotides within transcripts' exons.

mean_rps

This should be the number of reads per sample in total for use in backing out the FPKM calculations.

threshold

only estimate parameters from transcripts with mean FPKM measurements at least as large as threshold.

Value

A matrix of counts with the same number of rows and columns as the ballgown object

Details

If transcripts/exons are represented by GRanges or GRangesList objects, the width function is really useful in calculating transcript lengths.

Examples

library(ballgown)
  data(bg)
  countmat = fpkm_to_counts(bg, mean_rps=400000)