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

Description Usage Arguments Value Examples

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:

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

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## 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

Examples

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## 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 April 21, 2021, 9:46 a.m.