Combine multiple dosage matrix to a single genome-wide dosage

Inputs are VCF files, one for each chromosome presumably.

createGenomewideDosage(pathIn, chroms, nameOfchromWiseDosageFiles)

Arguments

nameOfchromWiseDosageFiles

Value

Output is an .rds (R dataset) format.

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

See also

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