This function is a part of the post-imputation quality control process prior to GWAS. This tests for Hardy-Weinberg Equilibrium (HWE) for X-chromosome variants in females. Males' hemizygous X chromosome prevents testing for HWE on their haploid X calls, and testing for HWE across all samples would have a high failure rate. This function will check for HWE across the X in females (cases and controls combined), following the recommendation in Khramtsova et al., 2023, and can remove these regions from analysis in all samples. The p-value threshold for filtering out SNPs is 0.05/no.of. X-chromosome variants.
Usage
Xhwe(DataDir, ResultDir = tempdir(), finput, filterSNP = TRUE, foutput)Arguments
- DataDir
Character string for the file path of the input PLINK binary files.
- ResultDir
Character string for the file path where all output files will be stored. The default is
tempdir().- finput
Character string, specifying the prefix of the input PLINK binary files.
- filterSNP
Boolean value,
TRUEorFALSEfor filtering out the X-chromosome variants i.e., SNPs from the input file or not (i.e., only flagged). The default isFALSE.- foutput
Character string, specifying the prefix of the output PLINK binary files if filtering option for the SNPs is chosen. The default is "FALSE".
Value
A list object containing SNPs. If filterSNP = TRUE, the output filtered PLINK binary files will be
produced inside DataDir.
Examples
DataDir <- GXwasR:::GXwasR_data()
ResultDir <- tempdir()
finput <- "GXwasR_example"
foutput <- "Test_output"
x <- Xhwe(
DataDir = DataDir, ResultDir = ResultDir,
finput = finput, foutput = foutput, filterSNP = TRUE
)
#> ✔ Output PLINK files, prefixed as female, are in /var/folders/d6/gtwl3_017sj4pp14fbfcbqjh0000gp/T//RtmpO7c0S8
#> This test is running on a case-control dataset with female samples.
#> ℹ Failed SNPs are excluded from the output PLINK files prefixed as Test_output is in /var/folders/d6/gtwl3_017sj4pp14fbfcbqjh0000gp/T//RtmpO7c0S8
x
#> [1] "rs56053951" "rs12353847" "rs5940058"