Occurrence of motifs in a set of ordered sequences

Description

Finds positions of sequence motif hits above a specified threshold in a list of sequences of the same length ordered by a provided index. Motif is specified by a position weight matrix (PWM) that contains estimated probability of base b at position i and is usually constructed via call to PWM function. Position of each motif hit 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 motif occurs.

Usage

motifScanHits(regionsSeq, motifPWM, minScore = "80%",
    seqOrder = c(1:length(regionsSeq)))

Arguments

Details

This function uses the matchPWM function to find matches to given motif in a set of input sequences. Only matches above specified minScore are considered as hits. 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 motif hits in the resulting matrix are returned as two-dimensional coordinates.

Value

The function returns a data.frame with positions of the motif hits 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 motif hits 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 motif hit within that sequence.

Author(s)

Vanja Haberle

See Also

plotMotifDensityMap
getPatternOccurrenceList

Examples

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

load(system.file("data", "TBPpwm.RData", package="seqPattern"))

motifOccurrence <- motifScanHits(regionsSeq = zebrafishPromoters,
                                motifPWM = TBPpwm, minScore = "85%",
                                seqOrder = order(promoterWidth))
head(motifOccurrence)

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
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> library(seqPattern)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/seqPattern/motifScanHits.Rd_%03d_medium.png", width=480, height=480)
> ### Name: motifScanHits
> ### Title: Occurrence of motifs in a set of ordered sequences
> ### Aliases: motifScanHits motifScanHits,DNAStringSet,matrix-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
> 
> load(system.file("data", "TBPpwm.RData", package="seqPattern"))
> 
> motifOccurrence <- motifScanHits(regionsSeq = zebrafishPromoters,
+                                 motifPWM = TBPpwm, minScore = "85%",
+                                 seqOrder = order(promoterWidth))
There were 12 warnings (use warnings() to see them)
> head(motifOccurrence)
  sequence position value
1        1       76     1
2        1      227     1
3        1      288     1
4        1      290     1
5        1      298     1
6        1      643     1
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>