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 1.5.0 Index]