phastBias: phastBias

Description Usage Arguments Details Value Author(s)

View source: R/bgc.R

Description

PhastBias performs a phylo-HMM analysis which assesses the evidence for GC-biased gene conversion (gBGC) on a particular branch of the tree.

Usage

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phastBias(align, mod, foreground = NULL, do.bgc = TRUE, bgc = 3,
  estimate.bgc = FALSE, bgc.expected.length = 1000,
  estimate.bgc.expected.length = FALSE, bgc.target.coverage = 0.01,
  estimate.bgc.target.coverage = TRUE, sel = -2.01483,
  cons.expected.length = 45, cons.target.coverage = 0.3,
  estimate.scale = FALSE, post.probs = TRUE)

Arguments

align

An msa object representing an alignment

mod

An object of type tm representing the neutral nucleotide substitution model.

foreground

A character string giving the name of a branch (or a label given to several branches) indicating which branch should be in the foreground. The foreground branch is where gBGC is tested.

do.bgc

If FALSE, do not model GC-biased gene conversion

bgc

Initial value for gBGC parameter B

estimate.bgc

If FALSE, do not optimize the gBGC parameter, just hold it at its initial value.

bgc.expected.length

Initial value for expected length of gBGC tract lengths.

estimate.bgc.expected.length

If FALSE, do not optimize the transition rate out of gBGC states (which determines the distribution of gBGC tract lengths)

bgc.target.coverage

Initial value for prior expected target coverage of gBGC tracts (as a fraction between 0 and 1).

estimate.bgc.target.coverage

If FALSE, constrain the rates into and out of gBGC state so that bgc.target.coverage does not change.

sel

Set the scaling factor for the conserved state. This is a population genetic parameter which translates to a scaling factor of sel/(1-exp(-sel)). The default value of s=-2.01483 translates to a scaling factor of 0.31 in the background branches.

cons.expected.length

Set the expected length of conserved elements.

cons.target.coverage

Set the target coverage for conserved elements.

estimate.scale

If TRUE, estimate a scaling factor for the branch lengths in all states.

post.probs

If TRUE, return value will include a data frame containing posterior probabilities for every position in the alignment and every state. Set to FALSE to suppress.

Details

PhastBias utilizes a HMM with the following states: neutral, conserved, neutral with gBGC, and conserved with gBGC. The scaling factor between conserved/neutral, the strength of gBGC, and the transition rates between states can be configured. It produces posterior probabilities for each state for every column of the alignment, or a set of gBGC "tracts" giving the regions where gBGC is predicted (by thresholding the posterior probability at 0.5).

Value

A list containing parameter estimates, a features object predicting which part of the alignments have gBGC probability > 0.5, and a data frame with posterior probabilities at all positions (if post.probs==TRUE)

Author(s)

Melissa J. Hubisz


rphast documentation built on May 1, 2019, 9:26 p.m.