importRankings: Import the motif databases for RcisTarget.

Description Usage Arguments Value Examples

View source: R/00_importRankings.R

Description

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

Usage

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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 take the first column.

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: #'

Examples

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## Loading from a .feather or .parquet file:
#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

aertslab/RcisTarget documentation built on April 21, 2021, 9:46 a.m.