sequenceReport,MotifEnrichmentResults-method {PWMEnrich} | R Documentation

## Generate a motif enrichment report for a single sequence

### Description

Generate a motif enrichment report for a single sequence

### Usage

    ## S4 method for signature 'MotifEnrichmentResults'
    sequenceReport(obj, seq.id, bg = TRUE, ...)

### Arguments

`obj` | a MotifEnrichmentResults object
`seq.id` | the sequence index or name
`bg` | if to use background corrected P-values to do the ranking (if available)
`...` | unused

### Value

a MotifEnrichmentReport object containing a table with the following columns:

- 'rank' - The rank of the PWM's enrichment in the sequence

- 'target' - The name of the PWM's target gene, transcript or protein complex.

- 'id' - The unique identifier of the PWM (if set during PWM creation).

- 'raw.score' - The raw score before P-value calculation

- 'p.value' - The P-value of motif enrichment (if available)

### 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)

       # reports for the two sequences
       r1 = sequenceReport(res, 1)
       r2 = sequenceReport(res, 2)

       # view the results
       r1
       r2

       # plot the top 10 most enriched motifs in the first, and then second sequence
       plot(r1[1:10])
       plot(r2[1:10])

    }

[Package PWMEnrich version 4.26.0 Index]