diffAnalyses {psichomics}R Documentation

Perform statistical analyses

Description

Perform statistical analyses

Usage

diffAnalyses(data, groups = NULL, analyses = c("wilcoxRankSum",
  "ttest", "kruskal", "levene", "fligner"), pvalueAdjust = "BH",
  geneExpr = NULL, psi = NULL)

Arguments

data

Data frame or matrix: gene expression or alternative splicing quantification

groups

Named list of characters (containing elements belonging to each group) or character vector (containing the group of each individual sample); if NULL, sample types are used instead when available, e.g. normal, tumour and metastasis

analyses

Character: statistical tests to perform (see Details)

pvalueAdjust

Character: method used to adjust p-values (see Details)

geneExpr

Character: name of the gene expression dataset (only required for density sparklines available in the interactive mode)

psi

Data frame or matrix: alternative splicing quantification (defunct argument, use data instead)

Details

The following statistical analyses may be performed by including the respective string in the analysis argument:

The following methods for p-value adjustment are supported by using the respective string in the pvalueAdjust argument:

Value

Table of statistical analyses

Examples

# Calculate PSI for skipped exon (SE) and mutually exclusive (MXE) events
eventType <- c("SE", "MXE")
annot <- readFile("ex_splicing_annotation.RDS")
junctionQuant <- readFile("ex_junctionQuant.RDS")

psi <- quantifySplicing(annot, junctionQuant, eventType=c("SE", "MXE"))
group <- c(rep("Normal", 3), rep("Tumour", 3))
diffAnalyses(psi, group)

[Package psichomics version 1.10.1 Index]