fpkm_to_counts: Turn FPKMs from a ballgown object into estimated counts for...
In alyssafrazee/polyester: Simulate RNA-seq reads

Turn FPKMs from a ballgown object into estimated counts for transcripts

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 `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`.

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

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

alyssafrazee/polyester documentation built on Sept. 17, 2021, 8:54 a.m.

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