bio3d (version 2.3-4)

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, ...)

Arguments

x

HMMER results as obtained from the function hmmer.

…

arguments passed to plot.blast.

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.

Details

See plot.blast for details.

References

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

See Also

hmmer, blast.pdb

Examples

# NOT RUN {
# HMMER server connection required - testing excluded

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

# }