Description Usage Arguments Value
the main function to call the VCF file and return the expected probabilities of the genotypes E(G_ij|D_ij) from VCF file
1 2 3 4 | vcf_process(file = "example/1g113low_1g56exomehigh_filtered.hg19.chr11_1000snps.vcf",
caseID_file = "example/caseID.txt", nhead = 128, ncol_ID = 9,
missing_th = 0.2, nvar_tot = 1000, nread = 300, maf_cut = 0.05,
common = TRUE)
|
file |
the VCF file |
caseID_file |
the caseID files |
nhead |
the row number of your VCF which contains all sample ID |
ncol_ID |
the number of columns before the sample ID |
missing_th |
the missing rate cut off for a SNP to be filtered, if missing>missing_th in case or controls, the SNP will be removed |
nvar_tot |
should be the number of SNPs in your VCF file, but if VCF is too large, you can choose only read in the first nsnp SNPs |
nread |
the number of SNPs read each time by R (nread<=nsnp) |
maf_cut |
the MAF to be used to filter out SNP, |
common |
Boolean variable to indicate common (TRUE) or rare (FALSE) variants |
a list for case or control (depends on group) including expected conditional probabilities, SNP info, Y, ncase/ncont etc
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