rankingRcisTarget-class: Class to store the motif databases for RcisTarget.

In aertslab/RcisTarget: RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions

Class to store the motif databases for RcisTarget.

Description

This class contains the rankings used by RcisTarget.

They are typically loaded from a .feather file with importRankings().

If the associated .descr file is available, it will also load the description of the database.

Class slots:

• rankings: data.frame (tbl_df) containing the rankings

• colType: 'gene'or 'region'

• rowType: 'motif' or the type of feature is stored (e.g. ChipSeq)

• org: human/mouse/fly

• genome: hg19, mm9, ...

• nColsInDB: Number of columns (e.g. genes/regions) available in the database (.feather file). Note that not all might be loaded in the current object.

• description: global description, summary, or any other information

• maxRank: Maximum ranking included in the database, higher values are converted to Inf.

Note that the main slot is @rankings, which is the one used by RcisTarget (it can accessed with getRanking()). The 'description' slots are mostly for user convenience.

Usage

## S4 method for signature 'rankingRcisTarget'
show(object)

## S4 method for signature 'rankingRcisTarget'
getRanking(object)

## S4 method for signature 'rankingRcisTarget'
nrow(x)

## S4 method for signature 'rankingRcisTarget'
ncol(x)

## S4 method for signature 'rankingRcisTarget'
colnames(x)

## S4 method for signature 'rankingRcisTarget'
rownames(x)

## S4 method for signature 'rankingRcisTarget'
getMaxRank(x)

## S4 method for signature 'rankingRcisTarget'
getNumColsInDB(x)

Arguments

object	[method: show] rankingRcisTarget object to show
x	[several methods] rankingRcisTarget object to apply the method

Value

• show: Prints a summary of the object

• getRanking: Returns the rankings

• ncol, nrow: Returns the number of columns or rows of the ranking

Examples

## Loading from a .feather file:
# dbFile <- "hg19-500bp-upstream-7species.mc9nr.feather"
# motifRankings <- importRankings(dbFile)
# motifRankings

## Loading a built object:
library(RcisTarget.hg19.motifDBs.cisbpOnly.500bp)
data("hg19_500bpUpstream_motifRanking_cispbOnly")
hg19_500bpUpstream_motifRanking_cispbOnly
class(hg19_500bpUpstream_motifRanking_cispbOnly)

aertslab/RcisTarget documentation built on March 7, 2024, 11:21 p.m.