msaTrim: Trimming multiple sequence alignments

Description

Trimming a multiple sequence alignment by discarding columns with too many gaps.

Usage

msaTrim(msa, gap.end = 0.5, gap.mid = 0.9)

Arguments

msa

A Fasta object containing a multiple alignment.

gap.end

Fraction of gaps tolerated at the ends of the alignment (0-1).

gap.mid

Fraction of gaps tolerated inside the alignment (0-1).

Value

The trimmed alignment is returned as a Fasta object.

Details

A multiple alignment is trimmed by removing columns with too many indels (gap-symbols). Any columns containing a fraction of gaps larger than gap.mid are discarded. For this reason, gap.mid should always be farily close to 1.0 therwise too many columns may be discarded, destroying the alignment.

Due to the heuristics of multiple alignment methods, both ends of the alignment tend to be uncertain and most of the trimming should be done at the ends. Starting at each end, columns are discarded as long as their fraction of gaps surpasses gap.end. Typically gap.end can be much smaller than gap.mid, but if set too low you risk that all columns are discarded!

Examples

Run this code

## Not run: 
# msa.file <- file.path(file.path(path.package("microseq"),"extdata"),"msa.fasta")
# msa <- readFasta(msa.file)
# print(nchar(msa$Sequence))
# msa.trimmed <- msaTrim(msa)
# print(nchar(msa.trimmed$Sequence))
# ## End(Not run)