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
)
an rds file and a ggplot graphic.
an object of class onemap
.
object of class vcfR;
path to VCF file.
a character specifying the first parent ID
a character specifying the second parent ID
the vcf parameter that store the allele depth information.
logical. If TRUE, all markers in vcf are consider, if FALSE only those in onemap.obj
a vector of characters specifying the markers names to be considered or NULL to consider all markers
a vector of characters specifying the individual names to be considered or NULL to consider all individuals
the graphic should contain the genotypes from onemap.obj or from the vcf? Specify using "onemap", "vcf" or "prob".
define the transparency of the dots in the graphic
rds file name to store the data frame with values used to build the graphic
set scale limit for y axis
set scale limit for x axis
If TRUE
, print tracing information.
Cristiane Taniguti, chtaniguti@tamu.edu
onemap_read_vcfR