vcfsToMDT: Convert a list of VCF objects into an MDT object

In olivmrtn/MachineLearningGWAS: Machine Learning for Genome Wide Association Studies

Description

Convert a list of VCF objects, each representing an individual patient, into a MDT object.

Usage

vcfsToMDT(vcfs, fill = 0L, verbose = TRUE)

## S4 method for signature 'list'
vcfsToMDT(vcfs, fill = 0L, verbose = TRUE)

Arguments

vcfs	List of VCF objects.
fill	Value for entries absent in VCF file. By default, sets to "0/0" corresponding to homozygote for REF allele.
verbose	logical specifying if function should be run in verbose mode.

Details

Please note that chromosome X, Y, XY and M/MT are replaced by integers 23, 24, 25 and 26. All other chromosome names are replaced by 99. Please use importPhenotype to fill in phenotype slot.

Value

MDT object with phenotype slot.

See Also

VCF readVcf readVcfDir importPhenotype

olivmrtn/MachineLearningGWAS documentation built on May 24, 2019, 12:52 p.m.