motifRankingForSequence,MotifEnrichmentResults-method {PWMEnrich} | R Documentation

## Get a ranking of motifs by their enrichment in one specific sequence

### Description

Get a ranking of motifs by their enrichment in one specific sequence

### Usage

    ## S4 method for signature 'MotifEnrichmentResults'
    motifRankingForSequence(
      obj,
      seq.id,
      bg = TRUE,
      id = FALSE,
      order = FALSE,
      rank = FALSE,
      unique = FALSE,
      ...
    )

### Arguments

`obj` | a MotifEnrichmentResults object
`seq.id` | either the sequence number or sequence name
`bg` | if to use background corrected P-values to do the ranking (if available)
`id` | if to show PWM IDs instead of target TF names
`order` | if to output the ordering of PWMs instead of actual P-values or raw values
`rank` | if the output should be rank of a PWM instead of actual P-values or raw values
`unique` | if TRUE, only the best rank is taken for each TF (only when id = FALSE, order = FALSE)
`...` | currently unused

### Value

a vector of P-values or raw enrichments sorted such that the first motif is most enriched

### Examples

    if(requireNamespace("PWMEnrich.Dmelanogaster.background")){
       ###
       # load the pre-compiled lognormal background
       data(PWMLogn.dm3.MotifDb.Dmel, package = "PWMEnrich.Dmelanogaster.background")

       # scan two sequences for motif enrichment
       sequences = list(DNAString("GAAGTATCAAGTGACCAGTAAGTCCCAGATGA"),
         DNAString("AGGTAGATAGAACAGTAGGCAATGAAGCCGATG"))
       res = motifEnrichment(sequences, PWMLogn.dm3.MotifDb.Dmel)

       # most enriched in the second sequences (sorted by lognormal background P-value)
       head(motifRankingForSequence(res, 2))

       # return unique TFs enriched in sequence 2
       head(motifRankingForSequence(res, 2, unique=TRUE))

       # sorted by raw affinity instead of P-value
       head(motifRankingForSequence(res, 2, bg=FALSE))

       # show IDs instead of target TF names
       head(motifRankingForSequence(res, 2, id=TRUE))

       # output the rank instead of P-value
       head(motifRankingForSequence(res, 2, rank=TRUE))
    }

[Package PWMEnrich version 4.28.1 Index]