phastBias: phastBias
In rphast: Interface to 'PHAST' Software for Comparative Genomics

Description Usage Arguments Details Value Author(s)

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

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)

`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.

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).

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)

Melissa J. Hubisz

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