prepare.trans.exp: Transcript expression preparation
In jmonlong/sQTLseekeR: Splicing QTL discovery tool

Description Usage Arguments Details Value Author(s)

Prepare the transcript expression matrix. Transcript with low expression are removed. Then gene expressing only one transcript are removed because not informative for splicing analysis. Finally the relative expression of the transcripts is retrieved and genes with low dispersion are removed. Also genes with just a few (<25) different splicing patterns are removed as they don't fit the permutation process.

1 2	prepare.trans.exp(te.df, min.transcript.exp = 0.01, min.gene.exp = 0.01, 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', then the values for each sample the other columns.
`min.transcript.exp`	the minimum transcript expression. Transcript 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.
`min.dispersion`	the minimum dispersion of the transcript relative expression. Genes with lower dispersion are removed.
`verbose`	If TRUE the names of filtered genes 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

jmonlong/sQTLseekeR documentation built on May 19, 2019, 1:54 p.m.