createGenomewideDosage: Combine multiple dosage matrix to a single genome-wide dosage

In wolfemd/genomicMateSelectR: Genomic Mate Selection

Combine multiple dosage matrix to a single genome-wide dosage

Description

Inputs are VCF files, one for each chromosome presumably.

Usage

createGenomewideDosage(pathIn, chroms, nameOfchromWiseDosageFiles)

Arguments

nameOfchromWiseDosageFiles

Details

Use common naming for VCF with prefix e.g. "chr12_".

Combines "<chroms>_<nameOfchromWiseDosageFiles>".

Output is an .rds (R dataset) format.

NOTICE: This function is part of a family of functions ("imputation_functions") developed as part of the NextGen Cassava Breeding Project genomic selection pipeline. For some examples of their useage:

• IITA_2021GS (should be first use of this package)

• NRCRI_2021GS

• TARI_2020GS

Value

Output is an .rds (R dataset) format.

See Also

Other imputation_functions: convertDart2vcf(), convertVCFtoDosage(), filter_positions(), mergeVCFs(), postImputeFilterBeagle4pt1(), postImputeFilter(), runBeagle4pt1GL(), runBeagle5(), splitVCFbyChr()

wolfemd/genomicMateSelectR documentation built on July 1, 2022, 10:42 p.m.