addLogo: Add motif logo to RcisTarget results table

In RcisTarget: RcisTarget: Identify transcription factor binding motifs enriched on a gene list

Description

Adds a column containing the logo URL to RcisTarget results table. Note that Transfac-Pro logos cannot be shown.

Usage

addLogo(motifEnrDT, addHTML = TRUE, dbVersion = "v9", motifCol = "motif")

Arguments

motifEnrDT	Results from RcisTarget (data.table)
addHTML	Whether to add the HTML tag <img> around the URL or not (boolean).
dbVersion	For current databases (mc9nr) use "v9"
motifCol	Name of the column which contains the logo ID.

Value

Returns the results table with a new column: 'logo'. This column contains either a URL with the logo image, or the HTML code to show the logo [e.g. with datatable()].

See Also

See the package vignette for more examples: vignette("RcisTarget")

Examples

# Run the enrichment (or load previous results)
load(paste(file.path(system.file('examples', package='RcisTarget')),
           "motifEnrichmentTable_wGenes.RData", sep="/"))

# Add link to logo
newMotifErnTable <- addLogo(motifEnrichmentTable_wGenes)

# Show table
library(DT)
datatable(newMotifErnTable[,-c("enrichedGenes"), with=FALSE],
          escape = FALSE,
          filter="top",
          options=list(pageLength=5))

RcisTarget documentation built on Nov. 8, 2020, 6:57 p.m.