GDSFunction_ClusterVersion: "GDS_ClusterVersion"

In GDS: Genome-Wide Differential Splicing Detection

Description

The GDS_ClusterVersion performs the GDS model and was adapted for use on a HPC cluster. This function should be used with the GDS_ClusterVersion.R file and GDS_ClusterVersion.pbs script in the documentation folder of the package. After running this function on the cluster, the output files should be binded together with the CreateOutput function.

Usage

GDSFunction_ClusterVersion(geneData, nsim = 1000, geneID,
  informativeCalls = TRUE, alpha = 0.5)

Arguments

geneData	The data with as rows the probesets and as columns the samples. Note that the first column should contain the gene IDs and the second column the exon IDs
nsim	The number of iterations to perform.
geneID	A vector of the gene IDs.
informativeCalls	Logical. Should the I/NI calls method be perform before applying the GDS model?
alpha	The threshold for filtering in the I/NI calls method. Probesets with scores higher than alpha are kept.

Value

A .RData file will be saved for each gene with the elements returned by the inigds and gds functions.

GDS documentation built on May 2, 2019, 6:09 p.m.