pathwaySummary: Pathway Summary Statistics

In pouryany/PanomiR: Detection of miRNAs that regulate interacting groups of pathways

Pathway Summary Statistics

Description

Generates a table of pathway activity profiles per sample

Usage

pathwaySummary(
  exprsMat,
  pathwayRef,
  id = "ENSEMBL",
  zNormalize = FALSE,
  method = FALSE,
  deGenes = NULL,
  trim = 0,
  tScores = NULL
)

Arguments

exprsMat	Gene expression matrix with row names as genes and samples as columns.
pathwayRef	Table of pathway-gene associations. Created from pathwayGeneTab function.
id	Gene annotation type in the row name of gene expression data.
zNormalize	Normalization of pathway summary score.
method	Choice of how to summarize gene ranks into pathway statistics.
deGenes	List of differentially expressed genes along with t-scores. Only necessary if working on Top 50% summary method.
trim	Percentage of top and bottom ranked genes to be excluded from pathway summary statistics.
tScores	Argument for-top-50-percent-genes method.

Value

pathExp Table of pathway activity profiles per sample.

Examples

pathTab <- tibble::tribble(
 ~Pathway, ~ENTREZID,  ~ENSEMBL,
 "Path1",   "125",      "ENSG00000196616",
 "Path1",   "3099",     "ENSG00000159399",
 "Path2",   "5230",     "ENSG00000102144",
 "Path2",   "5162",     "ENSG00000168291"
 )
exprsMat <- matrix(2 * (seq_len(12)), 4, 3)
rownames(exprsMat) <- pathTab$ENSEMBL
colnames(exprsMat) <- LETTERS[seq_len(3)]
pathwaySummary(exprsMat, pathTab, method = "x2")

pouryany/PanomiR documentation built on Aug. 20, 2022, 11:17 p.m.