transconc: Transcript Concentration

In harshsharma-cb/FASE: Analysis of RNA-Sequencing data using FASE (Finding Alternative Splicing Events).

Transcript Concentration

Description

Transcript concentration gives the abundance of transcripts expressed in different samples and conditions. It uses transcript structure generated by transtruct method and superimposes expression values of corresponding meta-features.

Usage

transconc(transtruct, designM)

Arguments

transtruct	transcript structure for EP/IP inclusion and exclusion for a gene.
designM	design matrix for the two conditions in question. It should be a binary matrix where 1 represents samples of the condition and 0 represents the samples of other condition.

Value

transconc returns three matrices:

1. transconc.samples: transcript concentration by samples.

2. transconc.condition: transcript concentration by condition.

3. transconc.TS: structures of transcripts and concentration of their meta-features, used for evaluating transcript abundance (transconc combines all structures by transtruct and retains only unique structures).

harshsharma-cb/FASE documentation built on Aug. 6, 2023, 1:37 a.m.