transcript_abundance: View transcript abundances

In CshlSiepelLab/tuSelecter2: Deconvolution of Expression for Nascent RNA Sequencing Data

View transcript abundances

Description

Produces a table with estimated trancript abundances for a given transcript_quantifier-class object.

Usage

transcript_abundance(tq, norm_method = c("tpm", "tmm"))

## S4 method for signature 'transcript_quantifier'
transcript_abundance(tq, norm_method = c("tpm", "tmm"))

Arguments

tq	A transcript_quantifier-class object
norm_method	type of normalization to use: "tpm" or "tmm". Defaults to "tpm". Described further in details.

Details

We provide two methods for normalizing transcript abundances, with each having different strengths. Both of the methods start with the polymerase desity ( polymerase per bp) estimated by the DENR method but handle sequencing depth differently:

• "tpm"Abundances are returned in the form analogous to TPM (transcripts per million) where the output units are normalized for sequencing depth by dividing the polymerase density by the total read count and multiplying by 10^6

• "tmm"Normalizes per transcript abundance using the inverse of the trimmed mean abundance for transcripts with abundance > 0. Uses transcripts in the 20 quantile range.

CshlSiepelLab/tuSelecter2 documentation built on June 2, 2025, 7:09 a.m.