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Make standard inputs for panvaR

make_panvar_inputs.Rd

Does some filtering of the genotype file for samples that have a phenotype and also minor allele frequency and snps with high missing rates. Will also calculate prinicpal components and optionally kinship matrix of the genotype file for use downstream in gwas.

Usage

make_panvar_inputs(
  genotype.path,
  phenotype.path,
  min.maf = 0.05,
  max.missing.snp = 0.1,
  calc.kinship = F,
  plink.path = NULL,
  out.dir = NULL,
  out.prefix = NULL,
  extra.plink.options = NULL
)

Arguments

genotype.path

character, path to genotype file, supported types: '.bed', .'vcf', '.vcf.gz'.

phenotype.path

character, path to table of phenotype to test. Expects samples (lines) in column 1 and phenotype in column 2. This is used to determine the set of samples (lines) to use in the analysis.

min.maf

numeric, filtering cutoff for minor allele frequency, snps are removed if they have maf less than this value. To ignore set to 0.

max.missing.snp

numeric, filtering cutoff for missing rate of snps, snps are removed if they have a missing rate higher than this. To ignore set to 1.

calc.kinship

boolean, optional, if TRUE, the kinship matrix will be calculated for use in mixed linear model gwas.

character, optional, path to plink2 executable. Will overide option set by set_plink_path.

out.dir

character, optional, path to store output. Will overide option set by set_out_dir.

out.prefix

character, optional, a prefix for output files. Will overide option set by set_panvar_prefix.

character, a vector of options to include in call to plink2. Should be a vector with plink2 arguments and their values as separate elements of vector. E.G. c("–max-maf", ".95", "–max-alleles", "2"). see snp_qc_plink

Value

Input files to be used for downstream panvaR functions. Stored in out.dir or the option set in set_out_dir. Runs snp_qc_plink to filter for maf and missing using plink2 and then rMVP::MVP.Data to prepare data for GWAS.

Examples

# work in progress