compareAgainstReference: Compare multiple methods and rank reference accordingly

In cTRAP: Identification of candidate causal perturbations from differential gene expression data

Description

Compare multiple methods and rank reference accordingly

Usage

compareAgainstReference(
  input,
  reference,
  method = c("spearman", "pearson", "gsea"),
  geneSize = 150,
  cellLines = NULL,
  cellLineMean = "auto",
  rankByAscending = TRUE,
  rankPerCellLine = FALSE
)

Arguments

input	Named numeric 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); or character of gene symbols composing a gene set that is tested for enrichment in reference data (only used if method includes gsea)
reference	Data matrix or perturbationChanges object (CMap perturbations; see prepareCMapPerturbations())
method	Character: one or more methods to compare data (spearman, pearson or gsea)
geneSize	Numeric: number of top up-/down-regulated genes to use as gene sets to test for enrichment in reference data; if a 2-length numeric vector, the first index is the number of top up-regulated genes and the second index is the number of down-regulated genes used to create gene sets; only used if method includes gsea and if input is not a gene set
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 when data for more than one cell line is available.
rankByAscending	Boolean: rank values based on their ascending (TRUE) or descending (FALSE) order?
rankPerCellLine	Boolean: rank results based on both individual cell lines and mean scores across cell lines (TRUE) or based on mean scores alone (FALSE)? If cellLineMean = FALSE, individual cell line conditions are always ranked.

Value

List of data frame containing the results per methods of comparison

cTRAP documentation built on Nov. 8, 2020, 10:58 p.m.