importRankings {RcisTarget}R Documentation

Import the motif databases for RcisTarget.

Description

The rankings are typically loaded from a .feather or .parquet file with importRankings().

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

Usage

importRankings(dbFile, columns = NULL, dbDescr = NULL)

Arguments

dbFile

.feather or .parquet file containing the rankings

columns

Columns to import from the .feather or .parquet file (e.g. only selected genes or regions)

dbDescr

The description fields are typically imported from the ".descr" file with the same filename as the dbFile. Otherwise they can be manually set e.g.:

dbDescr=list(colType="gene", rowType="motif", org="Human", genome="hg19", maxRank=Inf, description="")

Value

rankingRcisTarget object with the following slots: #'

Examples

## Loading from a .feather or .parquet file (the .descr file is read automatically):
#motifRankings<-importRankings("hg19-500bp-upstream-7species.mc9nr.feather")
#motifRankings<-importRankings("hg19-500bp-upstream-7species.mc9nr.parquet")

## The annotations for Motif collection 9 (sufix 'mc9nr')
# are already included in RcisTarget, and can be loaded with:
data(motifAnnotations_hgnc)

## For other versions, import the appropiate annotation. e.g.:
# annotDb <- importAnnotations("motifs-v9-nr.hgnc-m0.001-o0.0.tbl")
# optional: motifsInRanking <- getRanking(motifRankings)$features

[Package RcisTarget version 1.6.0 Index]