compareWithAllMethods {cTRAP} | R Documentation

## 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 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.
`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).

[Package cTRAP version 1.10.1 Index]