create_depths_profile function

Create database and ggplot graphic of allele reads depths

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.

Returns

an rds file and a ggplot graphic.

See Also

onemap_read_vcfR

Author(s)

Cristiane Taniguti, chtaniguti@tamu.edu