create_depths_profile: Create database and ggplot graphic of allele reads depths

In onemap: Construction of Genetic Maps in Experimental Crosses

Create database and ggplot graphic of allele reads depths

Description

Create database and ggplot graphic of allele reads depths

Usage

create_depths_profile(
  onemap.obj = NULL,
  vcfR.object = NULL,
  vcf = NULL,
  parent1 = NULL,
  parent2 = NULL,
  vcf.par = "AD",
  recovering = FALSE,
  mks = NULL,
  inds = NULL,
  GTfrom = "onemap",
  alpha = 1,
  rds.file = "data.rds",
  y_lim = NULL,
  x_lim = NULL,
  verbose = TRUE
)

Arguments

onemap.obj	an object of class onemap.
vcfR.object	object of class vcfR;
vcf	path to VCF file.
parent1	a character specifying the first parent ID
parent2	a character specifying the second parent ID
vcf.par	the vcf parameter that store the allele depth information.
recovering	logical. If TRUE, all markers in vcf are consider, if FALSE only those in onemap.obj
mks	a vector of characters specifying the markers names to be considered or NULL to consider all markers
inds	a vector of characters specifying the individual names to be considered or NULL to consider all individuals
GTfrom	the graphic should contain the genotypes from onemap.obj or from the vcf? Specify using "onemap", "vcf" or "prob".
alpha	define the transparency of the dots in the graphic
rds.file	rds file name to store the data frame with values used to build the graphic
y_lim	set scale limit for y axis
x_lim	set scale limit for x axis
verbose	If TRUE, print tracing information.

Value

an rds file and a ggplot graphic.

Author(s)

Cristiane Taniguti, [e-mail]

See Also

onemap_read_vcfR

onemap documentation built on June 8, 2025, 1:55 p.m.