plotHistMinAllelFreq: Minor allele frequencies

In timflutre/rutilstimflutre: Timothee Flutre's personal R code

Minor allele frequencies

Description

Plot the histogram of the minor allele frequency per SNP.

Usage

plotHistMinAllelFreq(
  X = NULL,
  mafs = NULL,
  main = NULL,
  xlim = c(0, 0.5),
  col = "grey",
  border = "white",
  las = 1,
  breaks = "FD",
  add.ml.beta = FALSE,
  verbose = 1,
  ...
)

Arguments

X	matrix of bi-allelic SNP genotypes encoded, for each SNP, in number of copies of its minor allele, i.e. as allele doses in [0,2], with genotypes in rows and SNPs in columns; if X is not NULL, minor allele frequencies will be estimated via estimSnpAf
mafs	vector of minor allele frequencies (not used if X is not NULL)
main	string for the main title
xlim	limits of the x-axis
col	color for the bars
border	color for the border of the bars
las	see ?par
breaks	see ?hist
add.ml.beta	if TRUE, add a curve corresponding to a Beta distribution with parameters inferred by maximum likelihood
verbose	verbosity level (0/1)
...	arguments to be passed to hist()

Value

invisible list with the output of hist and optim (if add.ml.beta=TRUE)

Author(s)

Timothee Flutre

timflutre/rutilstimflutre documentation built on Feb. 7, 2024, 8:17 a.m.