bio3d (version 2.4-4)

is.gap: Gap Characters

Description

Test for the presence of gap characters.

Usage

is.gap(x, gap.char = c("-", "."))

Value

Returns a logical vector with the same length as the input vector, or the same length as the number of columns present in an alignment input object ‘x’. In the later case TRUE elements corresponding to

‘gap.char’ matches in any alignment column (i.e. gap containing columns).

Arguments

x

an R object to be tested. Typically a sequence vector or sequence/structure alignment object as returned from seqaln, pdbaln etc.

gap.char

a character vector containing the gap character types to test for.

Author

Barry Grant

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

See Also

gap.inspect, read.fasta, read.fasta.pdb, seqaln, pdbaln

Examples

is.gap( c("G",".","X","-","G","K","S","T") )

if (FALSE) {
aln <- read.fasta( system.file("examples/kif1a.fa",
                   package = "bio3d") )

##- Print only non-gap positions (i.e. no gaps in any sequence)
aln$ali[, !is.gap(aln) ]

##- Mask any existing gaps with an "X"
xaln <- aln
xaln$ali[ is.gap(xaln$ali) ]="X"

##- Read a new PDB and align its sequence to the existing masked alignment
pdb <- read.pdb( "1mkj" )
seq2aln(pdbseq(pdb), xaln, id = "1mkj")
}