prepare.trans.exp: Transcript expression preparation
In guigolab/sQTLseekeR2: R package for splicing QTL mapping

Description Usage Arguments Details Value Author(s)

Prepare the transcript expression matrix. Transcripts with low expression are removed. Genes expressing only one transcript are removed because they are not informative for splicing analysis. The relative transcript expression is retrieved and genes with low variability in splicing are removed. Also genes with a small number (<25) of different splicing patterns are removed as they don't fit the permutation process.

prepare.trans.exp(
  te.df,
  min.transcript.exp = 0.01,
  min.gene.exp = 0.01,
  min.prop = 0.8,
  min.dispersion = 0.1,
  verbose = FALSE
)

`te.df`	a data.frame with the transcript expression. The first two columns are the transcript and gene ids, named 'trId' and 'geneId'. The rest of the columns contain the expression values for each sample.
`min.transcript.exp`	the minimum transcript expression. Transcripts with lower expression in all samples are removed.
`min.gene.exp`	the minimum gene expression. Samples with lower gene expression are removed from the analysis of this gene. If after this step the proportion of retained samples for a given gene is smaller than `min.prop` (see below), the gene is removed from the analysis.
`min.prop`	the minimum proportion of samples with gene expression above `min.gene.exp` for the gene to be analyzed.
`min.dispersion`	the minimum dispersion of the transcript relative expression. Genes with lower dispersion are removed.
`verbose`	If `TRUE` the names of filtered genes and transcripts will be displayed. Default is `FALSE`.

After removal of inappropriate transcripts/genes, transcript relative expression is computed by dividing its expression by the total expression of all transcripts for the gene.

a data.frame with the relative transcript expression for the genes to study.

Jean Monlong, Diego Garrido-Martín

guigolab/sQTLseekeR2 documentation built on Nov. 20, 2021, 3:21 a.m.