compareWithAllMethods: Compare reference using all methods

In nuno-agostinho/cTRAP: Identification of candidate causal perturbations from differential gene expression data

Compare reference using all methods

Description

Compare reference using all methods

Usage

compareWithAllMethods(
  method,
  input,
  reference,
  geneSize = 150,
  cellLines = NULL,
  cellLineMean = "auto",
  rankPerCellLine = FALSE,
  threads = 1,
  chunkGiB = 1,
  verbose = FALSE
)

Arguments

method	Character: comparison method (spearman, pearson or gsea; multiple methods may be selected at once)
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 character object with file path to CMap perturbations (see prepareCMapPerturbations()) or gene expression and drug sensitivity association (see loadExpressionDrugSensitivityAssociation())
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 rows with the mean of method across cell lines? If cellLineMean = "auto" (default), rows will be added when data for more than one cell line is available.
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.
threads	Integer: number of parallel threads
chunkGiB	Numeric: size (in gibibytes) of chunks to load reference file; only if argument reference is a file path
verbose	Boolean: print additional details?
rankByAscending	Boolean: rank values based on their ascending (TRUE) or descending (FALSE) order?

Value

List of data tables with correlation and/or GSEA score results

GSEA score

When method = "gsea", weighted connectivity scores (WTCS) are calculated (https://clue.io/connectopedia/cmap_algorithms).

nuno-agostinho/cTRAP documentation built on March 28, 2024, 3:59 p.m.