compareAgainstL1000 {cTRAP} | R Documentation

## Compare against L1000 datasets

### Description

Compare against L1000 datasets

### Usage

    compareAgainstL1000(diffExprGenes, perturbations, cellLine,
      method = c("spearman", "pearson", "gsea"), geneSize = 150,
      pAdjustMethod = "BH")

### Arguments

`diffExprGenes` | Numeric: named vector of differentially expressed genes where the name of the vector are gene names and the values are a statistic that represents significance and magnitude of differentially expressed genes (e.g. t-statistics)
`perturbations` | `l1000perturbations` object: file with L1000 loaded perturbations (check `loadL1000perturbations`)
`cellLine` | Character: cell line(s)
`method` | Character: comparison method (`spearman`, `pearson` or `gsea`)
`geneSize` | Number: top and bottom differentially expressed genes to use for gene set enrichment (GSE) (only used if `method` is `gsea`)
`pAdjustMethod` | Character: method for p-value adjustment (for more details, see `p.adjust.methods`; only used if `method` is `spearman` or `pearson`)

### Value

Data table with correlation or GSEA results comparing differential gene expression values with those associated with L1000 perturbations

### Examples

    cellLine <- "HepG2"
    data("l1000perturbationsSmallMolecules")
    perturbations <- l1000perturbationsSmallMolecules
    data("diffExprStat")

    # Compare against L1000 using Spearman correlation
    compareAgainstL1000(diffExprStat, perturbations, cellLine,
                        method="spearman")

    # Compare against L1000 using Pearson correlation
    compareAgainstL1000(diffExprStat, perturbations, cellLine,
                        method="pearson")

    # Compare against L1000 using gene set enrichment analysis (GSEA)
    compareAgainstL1000(diffExprStat, perturbations, cellLine, method="gsea")

[Package cTRAP version 1.2.0 Index]