readSNPs: Read SNPs performing genome quality control.
In JakubBartoszewicz/RImaGen: Fast Voxelwise Genome-Wide Association Studies in R

Read SNPs performing genome quality control.

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readSNPs(plinkFiles, call.rate.cutoff = 0.95, maf.cutoff = 0.1,
  hwe.pval = 5.7e-07, min.group = 8, subjects = NULL, force.snps = NULL,
  forcedOnly = FALSE, outPath = NULL)

`plinkFiles`	Paths to the plink files.
`call.rate.cutoff`	Call rate cutoff value.
`maf.cutoff`	Minor allele frequency cutoff value.
`hwe.pval`	Hardy-Weinberg equilibrium p-value cutoff value.
`min.group`	Minimum subjects per genotype group. Note that it can be only theoretically derived from MAF under H-W equilibrium assumption. Set to 0 to rely solely on the HWE test.
`subjects`	Vector of subject IDs to read data for.
`force.snps`	`character` vector of SNPs forced to be analysed even if not passing the quality control.
`forcedOnly`	`logical`. If `TRUE`, only the SNPs of interest will be analysed, regardless of their data quality.
`outPath`	A character string giving the base filename for optional output of QC-ed data. The extensions .bed, .bim, and .fam are appended to this string to give the filenames of the three output files.