| diffAnalyses {psichomics} | R Documentation |
Perform statistical analyses
diffAnalyses(data, groups = NULL, analyses = c("wilcoxRankSum", "ttest",
"kruskal", "levene", "fligner"), pvalueAdjust = "BH", geneExpr = NULL,
psi = NULL)
diffAnalysis(data, groups = NULL, analyses = c("wilcoxRankSum", "ttest",
"kruskal", "levene", "fligner"), pvalueAdjust = "BH", geneExpr = NULL,
psi = NULL)
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 |
The following statistical analyses may be performed by including the
respective string in the analysis argument:
ttest - Unpaired t-test (2 groups)
wilcoxRankSum - Wilcoxon Rank Sum test (2 groups)
kruskal - Kruskal test (2 or more groups)
levene - Levene's test (2 or more groups)
fligner - Fligner-Killeen test (2 or more groups)
density - Sample distribution per group (only usable
through the visual interface)
The following methods for p-value adjustment are supported by using the
respective string in the pvalueAdjust argument:
none: do not adjust p-values
BH: Benjamini-Hochberg's method (false discovery rate)
BY: Benjamini-Yekutieli's method (false discovery rate)
bonferroni: Bonferroni correction (family-wise error rate)
holm: Holm's method (family-wise error rate)
hochberg: Hochberg's method (family-wise error rate)
hommel: Hommel's method (family-wise error rate)
Table of statistical analyses
# 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)