onemap (version 3.0.0)

onemap_read_vcfR: Convert vcf file to onemap object

Description

Converts data from a vcf file to onemap initial object, while identify the appropriate marker segregation patterns.

Usage

onemap_read_vcfR(
  vcf = NULL,
  vcfR.object = NULL,
  cross = c("outcross", "f2 intercross", "f2 backcross", "ri self", "ri sib"),
  parent1 = NULL,
  parent2 = NULL,
  f1 = NULL,
  only_biallelic = TRUE,
  output_info_rds = NULL,
  verbose = TRUE
)

Value

An object of class onemap, i.e., a list with the following components:

geno

a matrix with integers indicating the genotypes read for each marker. Each column contains data for a marker and each row represents an individual.

n.ind

number of individuals.

n.mar

number of markers.

segr.type

a vector with the segregation type of each marker, as strings.

segr.type.num

a vector with the segregation type of each marker, represented in a simplified manner as integers, i.e. 1 corresponds to markers of type "A"; 2 corresponds to markers of type "B1.5"; 3 corresponds to markers of type "B2.6"; 4 corresponds to markers of type "B3.7"; 5 corresponds to markers of type "C.8"; 6 corresponds to markers of type "D1" and 7 corresponds to markers of type "D2". Markers for F2 intercrosses are coded as 1; all other crosses are left as NA.

input

the name of the input file.

n.phe

number of phenotypes.

pheno

a matrix with phenotypic values. Each column contains data for a trait and each row represents an individual.

error

matrix containing HMM emission probabilities

Arguments

vcf

string defining the path to VCF file;

vcfR.object

object of class vcfR;

cross

type of cross. Must be one of: "outcross" for full-sibs; "f2 intercross" for an F2 intercross progeny; "f2 backcross"; "ri self" for recombinant inbred lines by self-mating; or "ri sib" for recombinant inbred lines by sib-mating.

parent1

string specifying sample ID of the first parent. If f2 backcross population, define here the ID of the backcrossed parent.

parent2

string specifying sample ID of the second parent.

f1

string if you are working with f2 intercross or backcross populations you may have f1 parents in you vcf, specify its ID here

only_biallelic

if TRUE (default) only biallelic markers are considered, if FALSE multiallelic markers are included.

output_info_rds

define a name for the file with alleles information.

verbose

A logical, if TRUE it output progress status information.

Author

Cristiane Taniguti,

Details

Only biallelic SNPs and indels for diploid variant sites are considered.

Genotype information on the parents is required for all cross types. For full-sib progenies, both outbred parents must be genotyped. For backcrosses, F2 intercrosses and recombinant inbred lines, the original inbred lines must be genotyped. Particularly for backcross progenies, the recurrent line must be provided as the first parent in the function arguments.

Marker type is determined based on parental genotypes. Variants for which parent genotypes cannot be determined are discarded.

Reference sequence ID and position for each variant site are also stored.

See Also

read_onemap for a description of the output object of class onemap.

Examples

# \donttest{
data <- onemap_read_vcfR(vcf=system.file("extdata/vcf_example_out.vcf.gz", package = "onemap"),
                 cross="outcross",
                 parent1=c("P1"),
                 parent2=c("P2"))
# }