Plot a Summary of HMMER Hit Statistics.
Produces a number of basic plots that should facilitate hit selection from the match statistics of a HMMER result.
## S3 method for class 'hmmer' plot(x, ...)
x |
HMMER results as obtained from the function
|
... |
arguments passed to |
See plot.blast for details.
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. |
Barry Grant, Lars Skjaerven
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
## Not run:
# HMMER server connection required - testing excluded
##- PHMMER
seq <- get.seq("2abl_A", outfile = tempfile())
res <- hmmer(seq, db="pdb")
plot.hmmer(res)
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