create_depths_profile {onemap}

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