is.gap {bio3d}R Documentation

Gap Characters

Description

Test for the presence of gap characters.

Usage

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

Arguments

x an R object to be tested.
gap.char a character vector containing the gap character types to test for.

Value

Returns a logical vector with the same length as the input ‘x’, with TRUE elements corresponding to ‘gap.char’ matches.

Note

During alignment, gaps are introduced into sequences that are believed to have undergone deletions or insertions with respect to other sequences in the alignment. These gaps, often referred to as indels, can be represented with ‘NA’, ‘-’ or ‘.’ characters.

This function provides a simple test for the presence of such characters, or indeed any set of user defined characters set by the ‘gap.char’ argument.

Author(s)

Barry Grant

References

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

See Also

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

Examples


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

## Not run: 
aln <- read.fasta( system.file("examples/kinesin_xray.fa",
                   package = "bio3d") )

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

##- Read a PDB and align its sequence to the existing alignment
pdb <- read.pdb( system.file("examples/1bg2.pdb", package="bio3d") )
pdbseq <- aa321(pdb$atom[pdb$calpha,"resid"])

seqaln.pair(seqbind(xaln$ali[1,], pdbseq))
## End(Not run)

[Package bio3d version 1.0-6 Index]