AverageExons: Average expression values based on unique eigenexon IDs

In alfredorago/FESTA: Flexible Exon-based Splicing and Transcription Annotation

Description

Average expression values based on unique eigenexon IDs

Usage

AverageExons(data = NULL, spliceID = NULL, splicingRatios = F,
  NAcorrection = F)

Arguments

data	A data.frame or numeric matrix with one row per exon and one column per sample, containing the expression values of each exon.
spliceID	A data.frame. Output from the ClusterExons function.
splicingRatios	Logical. If FALSE, expression from all entries is reported on the same scale. If TRUE, expression from splicing entries is normalized by their gene's constitutive expression score, generating splicing ratios.
NAcorrection:	Logical. Applicable only if splicingRatios = TRUE. If TRUE, splicing ratios higher than 1 are set to 1 and NA/NaN/infinity values are set to 0. This accounts for experimental error in measurements.

Value

A data.frame with one column per sample and one row per exon group. If splicingRatios = F, entries report the average expression of all exons in the exon group. If splicingRatios = T, constitutive exon groups report the average expression of their exons and facultative exons report their average expression normalized to the average expression of their gene's constitutive exons group (splicing ratio).

Examples

 ExonAssignment = ClusterExons(data = SIRV_data$tpm, exonID = SIRV_data$ID)
 AverageExons(SIRV_data$tpm, ExonAssignment)

alfredorago/FESTA documentation built on May 24, 2019, 9:50 a.m.