importRankings: Import the motif databases for RcisTarget.

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

Import the motif databases for RcisTarget.

Description

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

Usage

importRankings(
  dbFile,
  indexCol = NULL,
  colType = "gene",
  columns = NULL,
  warnMissingColumns = TRUE,
  dbDescr = NULL
)

getRowNames(dbFile, indexCol = NULL)

getColumnNames(dbFile)

Arguments

dbFile	.feather or .parquet file containing the rankings
indexCol	Column name containing the feature IDs (e.g. motif names or chip-seq tracks). If NULL, it will try to use 'motifs', 'tracks', or 'features'.
colType	Colum type. i.e.:'gene'or 'region'
columns	Columns to load from the .feather or .parquet file (e.g. to read only specific genes or regions)
warnMissingColumns	If 'columns' is provided, warn if any ID is not available in the rankings?
dbDescr	Description fields (not used in the analysis, just for convenience of the user) e.g.: dbDescr=list(colType="gene", rowType="motif", org="Human", genome="hg19", maxRank=Inf, description="")

Value

rankingRcisTarget object with the following slots: #'

• rankings: data.frame containing the rankings

• colType: 'gene'or 'region'

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

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

• org: human/mouse/fly

• genome: hg19, mm9, ...

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

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

Examples

## Loading from a .feather or .parquet file:
# dbFilePath = "hg38_10kbp_up_10kbp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather"
# motifRankings<-importRankings(dbFilePath)

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

## For other versions, import the appropiate annotation. e.g.:
# annotDb <- importAnnotations("motifs-v10nr_clust-nr.hgnc-m0.001-o0.0.tbl")
# optional: motifsInRanking <- getRanking(motifRankings)$motifs

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