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

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"]])

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> library(seqPattern)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/seqPattern/getPatternOccurrenceList.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getPatternOccurrenceList
> ### Title: Occurrence of sequence patterns in a set of ordered sequences
> ### Aliases: getPatternOccurrenceList
> ###   getPatternOccurrenceList,DNAStringSet-method
> 
> ### ** Examples
> 
> library(GenomicRanges)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
> 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)
[1] "TA" "GC"
> head(patternsOccurrence[["GC"]])
  sequence position value
1        1       16     1
2        1       33     1
3        1       48     1
4        1       98     1
5        1      114     1
6        1      118     1
> 
> # motif consensus sequence
> patternsOccurrence <- getPatternOccurrenceList(regionsSeq = zebrafishPromoters,
+                     patterns = "TATAWAWR", seqOrder = order(promoterWidth))
> names(patternsOccurrence)
[1] "TATAWAWR"
> head(patternsOccurrence[["TATAWAWR"]])
  sequence position value
1        2       54     1
2        2       56     1
3        2       58     1
4        2       60     1
5        2       62     1
6        2       64     1
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>