compareAgainstReferencePerMethod {cTRAP}R Documentation

Compare single method

Description

Compare single method

Usage

compareAgainstReferencePerMethod(method, diffExprGenes, reference,
  geneSize = 150, cellLines = NULL, cellLineMean = "auto",
  rankPerCellLine = FALSE)

Arguments

method

Character: comparison methods to run (spearman, pearson or gsea); multiple methods can be selected

diffExprGenes

Numeric: named vector of differentially expressed genes whose names are gene identifiers and respective values are a statistic that represents significance and magnitude of differentially expressed genes (e.g. t-statistics)

reference

Data matrix or perturbationChanges object (CMap perturbations; read prepareCMapPerturbations)

geneSize

Number: top and bottom number of differentially expressed genes for gene set enrichment (only used if method = gsea)

cellLines

Integer: number of unique cell lines

cellLineMean

Boolean: add a column with the mean score across cell lines? If cellLineMean = "auto" (default) the mean score will be added if more than one cell line is available

rankPerCellLine

Boolean: when ranking results, also rank them based on individual cell lines instead of only focusing on the mean score across cell lines; if cellLineMean = FALSE, individual cell line conditions are always ranked

rankByAscending

Boolean: rank values based on their ascending (TRUE) or descending (FALSE) order?

Value

Data frame containing the results per method of comparison


[Package cTRAP version 1.4.0 Index]