msa (version 1.4.3)

msaCheckNames: Check and fix sequence names

Description

This function checks and fixed sequence names of multiple alignment objects if they contain characters that might lead to LaTeX problems when using msaPrettyPrint.

Usage

msaCheckNames(x, replacement=" ", verbose=TRUE)

Arguments

x

an object of class MultipleAlignment (which includes objects of classes MsaAAMultipleAlignment, MsaDNAMultipleAlignment, and MsaRNAMultipleAlignment)

replacement

a character string specifying with which character(s) potentially problematic characters should be replaced.

verbose

if TRUE (default), a warning message is shown if potentially problematic characters are found. Otherwise, the function silently replaces these characters (see details below).

Value

The function invisibly returns a copy of the argument x (therefore, an object of the same class as x), but with modified sequence/row names (see details above).

Details

The Biostrings package does not impose any restrictions on the names of sequences. Consequently, msa also allows all possible ASCII strings as sequence (row) names in multiple alignments. As soon as msaPrettyPrint is used for pretty-printing multiple sequence alignments, however, the sequence names are interpreted as plain LaTeX source code. Consequently, LaTeX errors may arise because of characters or words in the sequence names that LaTeX does not or cannot interpret as plain text correctly. This particularly includes appearances of special characters and backslash characters in the sequence names.

The msaCheckNames function takes a multiple alignment object and checks sequence names for possibly problematic characters, which are all characters but letters (upper and lower case), digits, spaces, commas, colons, semicolons, periods, question and exclamation marks, dashes, braces, single quotes, and double quotes. All other characters are considered problematic. The function allows for both checking and fixing the sequence names. If called with verbose=TRUE (default), the function prints a warning if a problematic character is found. At the same time, regardless of the verbose argument, the function invisibly returns a copy of x in whose sequence names all problematic characters have been replaced by the string that is supplied via the replacement argument (the default is a single space).

In any case, the best solution is to check sequence names carefully and to avoid problematic sequence names from the beginning.

References

http://www.bioinf.jku.at/software/msa U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter (2015). msa: an R package for multiple sequence alignment. Bioinformatics 31(24):3997-3999. DOI: 10.1093/bioinformatics/btv494.

See Also

msaPrettyPrint, MsaAAMultipleAlignment, MsaDNAMultipleAlignment, MsaRNAMultipleAlignment

Examples

## create toy example
mySeqs <- DNAStringSet(c("ACGATCGATC", "ACGACGATC", "ACGATCCCCC"))
names(mySeqs) <- c("Seq. #1", "Seq. \2", "Seq. ~3")

## perform multiple alignment
myAlignment <- msa(mySeqs)
myAlignment

## check names
msaCheckNames(myAlignment)

## fix names
myAlignment <- msaCheckNames(myAlignment, replacement="", verbose=FALSE)
myAlignment