variant_calls: Returns variant calls given a VSeqTools_pileup object

In SLeviyang/RegressHaplo: Haplotype Reconstruction Using Penalized Regression

Returns variant calls given a VSeqTools_pileup object

Description

Given a pileup, variants are called accorging to a frequency cutoff (min_freq) or a significance level(sig)

Usage

variant_calls(pu, min_freq = NULL, sig = NULL, heavy_tail = NULL)

Arguments

pu	a VSeqTools_pileup object returned by BAM_pileup
min_freq	Minimum frequency above which a variant is called.
sig	Significance levels above which a variant is called
heavy_tail	If T, use betabinomial error distribution, otherwise use poisson error distribution. Only relavent when !is.null(sig)

Details

Exactly one of min_freq and sig must be non-NULL. This determines whether cutoff or poisson algorithm is used.

Value

A VSeqTools_variant_call object which inherits the data.frame class. VSeqTools_variant_call objects are data.frames with columns pos, A, C, G, T, d, i. pos gives the position on the reference. Entries in other columns are logical depending on whether associated variant/deletion/insertion is called

SLeviyang/RegressHaplo documentation built on June 1, 2022, 10:48 p.m.