cmcalibrate: Calibrate a covariance model for searching

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

Calibrate a covariance model for searching

Description

Calibrate a covariance model for searching

Usage

cmcalibrate(
  cmfile,
  length = 1.6,
  forecast = FALSE,
  nforecast = NULL,
  memreq = FALSE,
  gtailn = 250,
  ltailn = 750,
  tailp = NULL,
  hfile = NULL,
  sfile = NULL,
  qqfile = NULL,
  ffile = NULL,
  xfile = NULL,
  seed = 181L,
  beta = 1e-15,
  nonbanded = FALSE,
  nonull3 = FALSE,
  random = FALSE,
  gc = NULL,
  cpu = NULL,
  mpi = FALSE,
  quiet = FALSE
)

Arguments

cmfile	(character file name) Filename of the CM to calibrate. calibration data will be added to this file.
length	(numeric scalar) Total length of random sequences to search, in megabases. (parameter "-L" to cmcalibrate)
forecast	(logical flag) Predict the running time of the calibration of cmfile (with provided options) on the current machine and exit. The calibration is not performed.
nforecast	(integer count) With forecast, specify the number of processors that will be used for the calibration.
memreq	(logical flag) Predict the amount of required memory for calibrating cmfile (with provided options) on the current machine and exit. The calibration is not performed.
gtailn	(numeric scalar) Fit the exponential tail for glocal Inside and glocal CYK to the n highest scores in the histogram tail, where n is gtailn times length (the number of Mb searched).
ltailn	(numeric scalar) Fit the exponential tail for local Inside and local CYK to the n highest scores in the histogram tail, where n is ltailn times length (the number of Mb searched).
tailp	(numeric scalar) Ignore gtailn and ltailn options and fit the tailp fraction tail of the histogram to an exponential tail, for all search modes.
hfile	(character file name) File to save the histograms fit.
sfile	(character file name) File to save the survival plot information.
qqfile	(character file name) File to save the quantile-quantile plot information.
ffile	(character file name) File to save the statistics of different exponential fits.
xfile	(character file name) File to save a list of the scores in each fit histogram.
seed	(non-negative integer scalar) Random number seed. 0 seeds the random number generator arbitrarily and non-reproducibly.
beta	(non-negative numeric scalar) Beta tail loss probability used for query-dependent banding (QDB).
nonbanded	(logical flag) If TRUE, turn off QDB during E-value calibration. This will slow down calibration.
nonull3	(logical flag) If TRUE, turn off the null3 post hoc additional null model. This is not recommended unless you plan on using the same option to cmsearch and/or cmscan.
random	(logical flag) If TRUE, use the background null model of the CM to generate the random sequences, instead of the more realistic HMM.
gc	(character file name) A file to use to determine the nucleotide frequencies for the random sequences.
cpu	(integer count) The number of parallel workers to use.
mpi	(logical flag) If TRUE, run as an MPI parallel program.
quiet	(logical flag) If TRUE, suppress standard output of cmcalibrate.

Value

NULL, invisibly

brendanf/inferrnal documentation built on Feb. 4, 2023, 4:49 p.m.