plotL1000comparison {cTRAP} | R Documentation

## Plot L1000 data comparison

### Description

Plot L1000 data comparison

### Usage

    plotL1000comparison(object, perturbationID, topGenes = TRUE)

### Arguments

`object` | `L1000 comparison` object
`perturbationID` | Character: perturbation identifier
`topGenes` | Boolean: plot top (`topGenes = TRUE`) or bottom genes (`topGenes = FALSE`) in case of plotting gene set enrichment analysis (GSEA)

### Value

Plot illustrating the comparison with L1000 data

### Examples

    data("l1000perturbationsKnockdown")
    cellLine <- "HepG2"
    compareKnockdown <- list()

    # Compare against L1000 using Spearman correlation
    compareKnockdown$spearman <- compareAgainstL1000(
        diffExprStat, l1000perturbationsKnockdown, cellLine, method="spearman")

    # Compare against L1000 using Pearson correlation
    compareKnockdown$pearson <- compareAgainstL1000(
        diffExprStat, l1000perturbationsKnockdown, cellLine, method="pearson")

    # Compare against L1000 using gene set enrichment analysis (GSEA) with the top
    # and bottom 150 genes
    compareKnockdown$gsea <- compareAgainstL1000(
        diffExprStat, l1000perturbationsKnockdown, cellLine, method="gsea",
        geneSize=150)

    EIF4G1knockdown <- grep("EIF4G1", compareKnockdown$gsea$genes, value=TRUE)
    plotL1000comparison(compareKnockdown$spearman, EIF4G1knockdown)
    plotL1000comparison(compareKnockdown$pearson, EIF4G1knockdown)
    plotL1000comparison(compareKnockdown$gsea, EIF4G1knockdown)

[Package cTRAP version 1.0.3 Index]