bbmix (version 1.0.0)

fit_bb: Fit beta binomial distribution to allelic counts for homozygous reference, heterozygous, homozygous alternative

Description

Fit beta binomial distribution to allelic counts for homozygous reference, heterozygous, homozygous alternative

Usage

fit_bb(
  counts_f,
  depth = 10,
  N = 1000,
  prefix = NULL,
  k = 3,
  alpha_p = c(1, 10, 499),
  beta_p = c(499, 10, 1),
  out,
  mc.cores = NULL
)

Value

saves stan object to file

Arguments

counts_f

file name with allele counts for SNPs

depth

depth cut-off to use to select SNPs to fit distributions

N

number of SNPs to use for fitting

prefix

charcter with prefix to add for saving files, defaults to NULL

k

number of components for mixture model, defaults to 3

alpha_p

alpha parameter for the k components of alpha parameter

beta_p

beta paramenter for the k components of Beta parameter

out

character with dir name to save output

mc.cores

number of cores to use, defaults to parallel detected cores

Examples

if (FALSE) {
## Retrive input files for running call_gt
counts_f <- system.file("extdata/input", "NA12878.chr22.Q20.allelicCounts.txt",
package = "bbmix",
mustWork = TRUE)

out <- tempdir()
fit_bb(counts_f = counts_f, N=10,
out = out, mc.cores=1)
unlink(out)
}