motifRankingForGroup,MotifEnrichmentResults-method {PWMEnrich} | R Documentation

## Get a ranking of motifs by their enrichment in the whole set of sequences

### Description

Get a ranking of motifs by their enrichment in the whole set of sequences

### Arguments

`obj` | a MotifEnrichmentResults object
`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 log(P-values), P-values or raw enrichments sorted such that the first motif is most enriched

### Examples

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

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

       # most enriched in both sequences (sorted by lognormal background P-value)
       head(motifRankingForGroup(res))

       # Return a non-redundant set of TFs
       head(motifRankingForGroup(res, unique=TRUE))

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

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

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

[Package PWMEnrich version 4.18.0 Index]