Description Usage Arguments Details Value Author(s) Examples
View source: R/fpkm_to_counts.R
Turn FPKMs from a ballgown object into estimated counts for transcripts
1 2 | fpkm_to_counts(bg = NULL, mat = NULL, tlengths = NULL, mean_rps = 1e+08,
threshold = 0)
|
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 |
tlengths |
if using |
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 |
If transcripts/exons are represented by GRanges
or
GRangesList
objects, the width
function is really useful
in calculating transcript lengths.
A matrix of counts with the same number of rows and columns as the ballgown object
Jeff Leek
1 2 3 | library(ballgown)
data(bg)
countmat = fpkm_to_counts(bg, mean_rps=400000)
|
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