bio3d (version 2.3-3)

gap.inspect: Alignment Gap Summary

Description

Report the number of gaps per sequence and per position for a given alignment.

Usage

gap.inspect(x)

Arguments

x

a matrix or an alignment data structure obtained from read.fasta or read.fasta.pdb.

Value

Returns a list object with the following components:

row

a numeric vector detailing the number of gaps per row (i.e. sequence).

col

a numeric vector detailing the number of gaps per column (i.e. position).

t.inds

indices for gap containing coloums

f.inds

indices for non-gap containing coloums

bin

a binary numeric matrix with the same dimensions as the alignment, with 0 at non-gap positions and 1 at gap positions.

Details

Reports the number of gap characters per row (i.e. sequence) and per column (i.e. position) for a given alignment. In addition, the indices for gap and non-gap containing coloums are returned along with a binary matrix indicating the location of gap positions.

References

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

See Also

read.fasta, read.fasta.pdb

Examples

# NOT RUN {
aln <- read.fasta( system.file("examples/hivp_xray.fa",
                   package = "bio3d") )

gap.stats <- gap.inspect(aln$ali)
gap.stats$row # Gaps per sequence
gap.stats$col # Gaps per position
##gap.stats$bin # Binary matrix (1 for gap, 0 for aminoacid)
##aln[,gap.stats$f.inds] # Alignment without gap positions 

plot(gap.stats$col, typ="h", ylab="No. of Gaps") 
# }