Mask Highly Variable Regions of An Alignment

Description

Automatically masks poorly aligned regions of an alignment based on sequence conservation and gap frequency.

Usage

MaskAlignment(myXStringSet,
              windowSize = 5,
              threshold = 1,
              maxFractionGaps = 0.2,
              showPlot = FALSE)

Arguments

Details

Poorly aligned regions of a multiple sequence alignment may lead to incorrect results in downstream analyses, and require extra processing time. One method to mitigate their effects is to mask columns of the alignment that may be poorly aligned, such as highly-variable regions or regions with many insertions and deletions (gaps).

Highly variable regions are detected by their signature of having low information content. A moving average of windowSize nucleotides to the left and right of the center-point is applied to smooth noise in the information content signal along the sequence. Regions dropping below threshold bits or more than maxFractionGaps are masked in the returned alignment.

Value

A MultipleAlignment object of the input type with masked columns where the input criteria are met.

Author(s)

Erik Wright DECIPHER@cae.wisc.edu

See Also

AlignSeqs, IdClusters

Examples

fas <- system.file("extdata", "Streptomyces_ITS_aligned.fas", package="DECIPHER")
dna <- readDNAStringSet(fas)
masked_dna <- MaskAlignment(dna, showPlot=TRUE)

# display only unmasked nucleotides for use in downstream analyses
not_masked <- as(masked_dna, "DNAStringSet")
BrowseSeqs(not_masked)

# display only masked nucleotides that are covered by the mask
masked <- masked_dna
colmask(masked, append="replace", invert=TRUE) <- colmask(masked)
masked <- as(masked, "DNAStringSet")
BrowseSeqs(masked)

# display the complete DNA sequence set including the mask
masks <- lapply(width(colmask(masked_dna)), rep, x="+")
masks <- unlist(lapply(masks, paste, collapse=""))
masked_dna <- replaceAt(dna, at=IRanges(colmask(masked_dna)), value=masks)
BrowseSeqs(masked_dna)

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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> library(DECIPHER)
Loading required package: Biostrings
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: XVector
Loading required package: RSQLite
Loading required package: DBI
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/DECIPHER/MaskAlignment.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MaskAlignment
> ### Title: Mask Highly Variable Regions of An Alignment
> ### Aliases: MaskAlignment
> 
> ### ** Examples
> 
> fas <- system.file("extdata", "Streptomyces_ITS_aligned.fas", package="DECIPHER")
> dna <- readDNAStringSet(fas)
> masked_dna <- MaskAlignment(dna, showPlot=TRUE)
> 
> # display only unmasked nucleotides for use in downstream analyses
> not_masked <- as(masked_dna, "DNAStringSet")
> BrowseSeqs(not_masked)
> 
> # display only masked nucleotides that are covered by the mask
> masked <- masked_dna
> colmask(masked, append="replace", invert=TRUE) <- colmask(masked)
> masked <- as(masked, "DNAStringSet")
> BrowseSeqs(masked)
> 
> # display the complete DNA sequence set including the mask
> masks <- lapply(width(colmask(masked_dna)), rep, x="+")
> masks <- unlist(lapply(masks, paste, collapse=""))
> masked_dna <- replaceAt(dna, at=IRanges(colmask(masked_dna)), value=masks)
> BrowseSeqs(masked_dna)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>