tpms_to_expected_reads: Convert TPMs to Expected Fragments
In warrenmcg/absSimSeq: RNA-Seq Simulation with Absolute Counts

This function takes as input a matrix of transcript abundances (in TPMs) and converts them to expected fragments for each transcript in each condition. The expected reads is proportional to the effective length for the transcript and the expected size of the library.

1 2	tpms_to_expected_reads(trans_abund = NULL, eff_lens = NULL, mean_library_size = NULL)

`trans_abund,`	a N x 2 matrix or data frame of transcript abundances (in TPMs) for each transcript in each of two conditions.
`eff_lens,`	a vector of effective lengths for each transcript. the transcripts must be in the same order as what is found in `trans_abund`.
`mean_library_size,`	a single value of the expected size of the sequencing library (e.g. 60 million fragments)

a list with two entries:

expected_reads: an N x 2 matrix of the expected reads for each transcript in each condition
fold_changes: the perceived fold changes if one were to use the expected reads (unnormalized by library size or transcript effective length).

warrenmcg/absSimSeq documentation built on May 29, 2019, 9:57 a.m.