MaskAlignment: 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

myXStringSet

An AAStringSet, DNAStringSet, or RNAStringSet object of aligned sequences.

windowSize

Integer value specifying the size of the region to the left and right of the center-point to use in calculating the moving average.

threshold

Numeric giving the average entropy in bits from 0 to 2 below which a region is masked.

maxFractionGaps

Numeric specifying the maximum faction of gaps in an alignment column to be masked.

showPlot

Logical specifying whether or not to show a plot of the positions that were kept or masked.

Value

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

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.

Examples

Run this code

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)