getPatternOccurrenceList {seqPattern} | R Documentation

## Occurrence of sequence patterns in a set of ordered sequences

### Description

Finds positions of specified sequence patterns in a list of sequences of the same length ordered by a provided index. Sequence patterns can be consensus sequences of variable length and can contain IUPAC ambiguity code. Position of each pattern occurrence is specified in two-dimensional matrix, i.e. the first coordinate provides the ordinal number of the sequence and the second coordinate gives the position within the sequence where the pattern occurs.

### Usage

    getPatternOccurrenceList(regionsSeq, patterns, seqOrder =
            c(1:length(regionsSeq)), useMulticore = FALSE, nrCores = NULL)

### Arguments

`regionsSeq` | A `DNAStringSet` object. Set of sequences of the same length in which to search for the patterns.
`patterns` | Character vector specifying one or more DNA sequence patterns (oligonucleotides). IUPAC ambiguity codes can be used and will match any letter in the subject that is associated with the code.
`seqOrder` | Integer vector specifying the order of the provided input sequences. Must have the same length as the number of sequences in the `regionSeq`. The default value will order the sequences as they are ordered in the `regionSeq` object.
`useMulticore` | Logical, should multicore be used. `useMulticore = TRUE` is supported only on Unix-like platforms.
`nrCores` | Number of cores to use when `useMulticore = TRUE`. Default value `NULL` uses all detected cores.

### Details

This function uses the `matchPattern` function to find occurrences of given sequence patterns in a set of input sequences. Input sequences must all be of the same length and are ordered according to the index provided in the `seqOrder` argument, creating a `n * m` matrix, where `n` is the number of sequences and `m` is the length of the sequences. Positions of pattern matches in the resulting matrix are returned as two-dimensional coordinates.

### Value

The function returns a named list with one element for each sequence pattern specified in the `patterns` argument. Each element of the list is a `data.frame` with positions of the corresponding pattern in the set of input sequences. The input sequences of the same length are sorted according to the index in `seqOrder` argument and the positions of pattern matches in the resulting `n * m` matrix (where `n` is the number of sequences and `m` is the length of the sequence) are provided. The `sequence` column in the data.frame provides the ordinal number of the sequence in the ordered list of sequences and the `position` column provides the start position of the pattern match within that sequence.

### Author(s)

Vanja Haberle

### See Also

`plotPatternDensityMap`
`motifScanHits`

### Examples

    library(GenomicRanges)
    load(system.file("data", "zebrafishPromoters.RData", package="seqPattern"))
    promoterWidth <- elementMetadata(zebrafishPromoters)$interquantileWidth

    # dinucleotide patterns
    patternsOccurrence <- getPatternOccurrenceList(regionsSeq = zebrafishPromoters,
                        patterns = c("TA", "GC"), seqOrder = order(promoterWidth))
    names(patternsOccurrence)
    head(patternsOccurrence[["GC"]])

    # motif consensus sequence
    patternsOccurrence <- getPatternOccurrenceList(regionsSeq = zebrafishPromoters,
                        patterns = "TATAWAWR", seqOrder = order(promoterWidth))
    names(patternsOccurrence)
    head(patternsOccurrence[["TATAWAWR"]])

[Package seqPattern version 1.12.0 Index]