REIDSFunction_ClusterVersion: "REIDS_ClusterVersion"

In REIDS: Random Effects for the Identification of Differential Splicing

Description

The REIDS_ClusterVersion performs the REIDS model and was adapted for use on a HPC cluster. This function should be used with the REIDS_ClusterVersion.R file and REIDS_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

REIDSFunction_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 REIDS 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 iniREIDS and REIDS functions.

REIDS documentation built on May 2, 2019, 4:45 p.m.