compareAgainstReferencePerMethod: Compare single method

Description Usage Arguments Value

View source: R/compare.R

Description

Compare single method

Usage

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

Arguments

method

Character: one or more methods to compare data (spearman, pearson or gsea)

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())

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.

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.

rankByAscending

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

Value

Data frame containing the results per method of comparison


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