Description Usage Arguments Value
It will read the additive coding genotype file, filter out variants and then return the phenotype and genotype file necessary for association test.
It calls functions geno_add_2pheno
and filter_genocall
1 | geno_process(genofile, caseIDfile, missing_cut, maf_cut, common)
|
genofile |
additive coding genotype files, it is the .raw file in plink |
caseIDfile |
the file including the list of case IDs |
missing_cut |
a decimal, the missing rate cut off |
maf_cut |
a decimal, the minor allele cut off |
common |
a boolean variable, common = T, return the variants with maf>=maf_cut, ow, return variants with maf<maf_cut. |
a list including- geno: a matrix with the genotype data only (size of nsample*nsnp), snps: matrix with variant information, Y: a vector of phenotype corresponding to the order of the sample in geno, rm_call0: a vector including the position of variants with hom reference calls and rm_miss: a vector including the position of variants with missing_rate>missing_cut in snps after removing rm_call0.
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