bio3d (version 2.4-4)

plot.hmmer: Plot a Summary of HMMER Hit Statistics.

Description

Produces a number of basic plots that should facilitate hit selection from the match statistics of a HMMER result.

Usage

# S3 method for hmmer
plot(x, ...)

Value

Produces a plot on the active graphics device and returns a three component list object:

hits

an ordered matrix detailing the subset of hits with a normalized score above the chosen cutoff. Database identifiers are listed along with their cluster group number.

acc

a character vector containing the database accession identifier of each hit above the chosen threshold.

pdb.id

a character vector containing the database accession identifier of each hit above the chosen threshold.

inds

a numeric vector containing the indices of the hits relative to the input hmmer object.

Arguments

x

HMMER results as obtained from the function hmmer.

...

arguments passed to plot.blast.

Author

Barry Grant, Lars Skjaerven

Details

See plot.blast for details.

References

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

See Also

hmmer, blast.pdb

Examples

if (FALSE) {
# HMMER server connection required - testing excluded

##- PHMMER
seq <- get.seq("2abl_A", outfile = tempfile())
res <- hmmer(seq, db="pdb")
plot.hmmer(res)

}