Gap Characters
Test for the presence of gap characters.
is.gap(x, gap.char = c("-", "."))x |
an R object to be tested. Typically a sequence vector or
sequence/structure alignment object as returned from |
gap.char |
a character vector containing the gap character types to test for. |
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).
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.
Barry Grant
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
is.gap( c("G",".","X","-","G","K","S","T") )
## Not run:
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")
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.