cmbuild: Construct covariance model(s) from structually annotated...

In brendanf/inferrnal: Interface to Call Programs from Infernal RNA Covariance Model Package

Construct covariance model(s) from structually annotated alignment(s)

Description

Calls the standalone program cmbuild from the Infernal package, which must be installed. For more information about options, see the Infernal documentation.

Usage

cmbuild(
  msafile,
  cmfile_out,
  name = NULL,
  force = FALSE,
  summary_file = NULL,
  reannotated_msa = NULL,
  consensus_method = NULL,
  symfrac = NULL,
  rsearch = NULL,
  null = NULL,
  prior = NULL,
  weights = NULL,
  wid = NULL,
  eff_num = NULL,
  ere = NULL,
  eminseq = NULL,
  emaxseq = NULL,
  ehmmre = NULL,
  eset = NULL,
  p7ere = NULL,
  p7ml = FALSE,
  refine = NULL,
  local = FALSE,
  gibbs = FALSE,
  seed = NULL,
  cyk = FALSE,
  notrunc = FALSE,
  extra = NULL,
  quiet = TRUE
)

Arguments

msafile	(character filename) filename of MSA file to read.
cmfile_out	(character filename) filename to write CM to.
name	(character string) name of the CM (option -N to cmbuild). The default uses the name(s) given in the alignment file, or the name of the alignment file.
force	(logical scalar) overwrite cmfile_out if it exists.
summary_file	(character filename) filename to write summary output to.
reannotated_msa	(character filename) filename to write a reannotated alignment(s) to (option -O to cmbuild)
consensus_method	(one of "fast", "hand", or "noss") method to define consensus columns in alignment. (options --fast, --hand, and --noss to cmbuild)
symfrac	(integer scalar) residue fraction threshold necessary to define a consensus column.
rsearch	(character filename) RIBOSUM matrix to use in parameterizing emission scores.
null	(character filename) null model file.
prior	(character filename) Dirichlet prior file.
weights	(character; one of "wpb", "wgsc", "wnone", "wgiven", or "wblosum") sequence weighting method (options --wpb, --wgsc, --wnone, --wgiven, and --wblosum to cmbuild).
wid	(numeric scalar) percent identity for clustering when weights = "blosum".
eff_num	(character; one of "eent" or "enone") entropy weighting strategy (options --eent or --enone to cmbuild).
ere	(numeric scalar) target mean match state relative entropy.
eminseq	(numeric scalar) minimum allowed effective sequence number.
emaxseq	(numeric scalar) maximum allowed effective sequence number.
ehmmre	(numeric scalar) target HMM mean match state relative entropy.
eset	(numeric scalar) effective sequence number for entropy weighting.
p7ere	(numeric scalar) target mean match state relative entropy for the filter p7 HMM.
p7ml	(logical scalar) use a maximum liklihood p7 HMM built from the CM.
refine	(character filename) if given, the alignment is iteratively refined, and the final alignment is written to this file.
local	(logical scalar) use local alignment with refine (option -l to cmbuild).
gibbs	(logical scalar) use Gibbs sampling instead of maximum likelihood with refine.
seed	(integer scalar) pseudorandom number seed for Gibbs sampling.
cyk	(logical scalar) use the CYK alignment algorithm with refine.
notrunc	(logical scalar) turn off the truncated alignment algorithm with refine.
extra	(character) additional arguments to pass to cmbuild.
quiet	(logical scalar) do not print cmbuild output to the console.

Value

NULL, invisibly

Examples

    cmbuild(
        msafile = stk_5_8S(),
        cmfile_out = "/dev/null",
        force = TRUE,
        quiet = FALSE
    )

brendanf/inferrnal documentation built on Sept. 30, 2024, 6:40 a.m.