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

In bio3d: Biological Structure Analysis

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 class 'hmmer'
plot(x, ...)

Arguments

x	HMMER results as obtained from the function hmmer.
...	arguments passed to plot.blast.

Details

See plot.blast for details.

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.

Author(s)

Barry Grant, Lars Skjaerven

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)


## End(Not run)

bio3d documentation built on Oct. 30, 2024, 1:08 a.m.