ExonTesting: "ExonTesting"

In REIDS: Random Effects for the Identification of Differential Splicing

Description

The ExonTesting function performs a t-test (2 groups) or F-test (more than 2 groups) between the array scores of predefined groups. If specified, probe sets are filtered out on exon scores and significance level. The function is the internal function of ASExons.

Usage

ExonTesting(ExonScores, ArrayScores, Exonthreshold = NULL, Groups = list(),
  paired = FALSE, significancelevel = NULL)

Arguments

ExonScores	The path to the file with the exon scores of the probe sets.
ArrayScores	The path to the file with the array scores of the probe sets.
Exonthreshold	The exon score threshold to be maintained. If not NULL, probe sets with an exon score lower than this value are not considered further and the p-values will be adjusted for multiplicity after testing. If NULL, all probesets are considered and a multiplicity correction is not performed.
Groups	A list with elements specifying the columns of the data in each group.
paired	Logical. Are the groups paired? If TRUE the mean paired differences are calculated and tested whether these are significantly different from zero or not.
significancelevel	The significance level to be maintained on the p-values. The filtering on the significance is conducted only if an Exonthreshold is specified and the p-value are adjusted for multiplicity.

Value

A data frame with one line per exon. The columns contain the gene ID, the exon ID, the exon score, the test statistic, a p-value and an adjusted p-value. If the groups are paired also the mean paired difference is given. The p-values are adjusted for multiplicity and filtered on significance if significancelevel is not NULL.

REIDS documentation built on May 2, 2019, 6:42 a.m.