rankingRcisTarget-class {RcisTarget} | R Documentation

## Class to store the motif databases for RcisTarget.

### 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:

- rankings: data.frame (tbl_df) containing the rankings

- colType: 'gene'or 'region'

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

- org: human/mouse/fly

- genome: hg19, mm9, ...

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

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

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

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

    ## 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

- show: Prints a summary of the object

- getRanking: Returns the rankings

- ncol, nrow: Returns the number of columns or rows of the ranking

### Examples

    ## 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)

[Package RcisTarget version 1.12.0 Index]