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 1.2.0 Index]