groupReport,MotifEnrichmentResults-method {PWMEnrich} | R Documentation

## Generate a motif enrichment report for the whole group of sequences together

### Description

Generate a motif enrichment report for the whole group of sequences together

### Usage

    ## S4 method for signature 'MotifEnrichmentResults'
    groupReport(obj, top = 0.05, bg = TRUE, by.top.motifs = FALSE, ...)

### Arguments

`obj` | a MotifEnrichmentResults object
`top` | what proportion of top motifs should be examined in each individual sequence (by default 0.05, i.e. 5%)
`bg` | if to use background corrected P-values to do the ranking (if available)
`by.top.motifs` | if to rank by the proportion of sequences where the motif is within 'top' percentage of motifs
`...` | unused

### Value

a MotifEnrichmentReport object containing a table with the following columns:

- 'rank' - The rank of the PWM's enrichment in the whole group of sequences together

- '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)

- 'top.motif.prop' - The proportion (between 0 and 1) of sequences where the motif is within `top` proportion of enrichment motifs.

### 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)

       # produce a report for all sequences taken together
       r.default = groupReport(res)

       # produce a report where the last column takes top 1% motifs
       r = groupReport(res, top=0.01)

       # view the results
       r

       # plot the top 10 most enriched motifs
       plot(r[1:10])

    }

[Package PWMEnrich version 4.28.1 Index]