importRankings {RcisTarget} | R Documentation

## 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 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: #'

- 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:
    #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 1.14.0 Index]