Identity-by-descent
Quality Control based on Identity-by-descent (IBD) computed by PLINK 1.9 using its method-of-moments.
snp_plinkIBDQC( plink.path, bedfile.in, bedfile.out = NULL, pi.hat = 0.08, ncores = 1, pruning.args = c(100, 0.2), do.blind.QC = TRUE, extra.options = "", verbose = TRUE )
plink.path |
Path to the executable of PLINK 1.9. |
bedfile.in |
Path to the input bedfile. |
bedfile.out |
Path to the output bedfile. Default is created by
appending |
pi.hat |
PI_HAT value threshold for individuals (first by pairs)
to be excluded. Default is |
ncores |
Number of cores used. Default doesn't use parallelism. You may use nb_cores. |
pruning.args |
A vector of 2 pruning parameters, respectively
the window size (in variant count) and the pairwise $r^2$ threshold
(the step size is fixed to 1). Default is |
do.blind.QC |
Whether to do QC with |
extra.options |
Other options to be passed to PLINK as a string (for the IBD part). More options can be found at https://www.cog-genomics.org/plink/1.9/ibd. |
verbose |
Whether to show PLINK log? Default is |
The path of the new bedfile. If no sample is filter, no new bed/bim/fam files are created and then the path of the input bedfile is returned.
Chang, Christopher C, Carson C Chow, Laurent CAM Tellier, Shashaank Vattikuti, Shaun M Purcell, and James J Lee. 2015. Second-generation PLINK: rising to the challenge of larger and richer datasets. GigaScience 4 (1): 7. doi: 10.1186/s13742-015-0047-8.
## Not run:
bedfile <- system.file("extdata", "example.bed", package = "bigsnpr")
plink <- download_plink()
bedfile <- snp_plinkIBDQC(plink, bedfile,
bedfile.out = tempfile(fileext = ".bed"),
ncores = 2)
df_rel <- snp_plinkIBDQC(plink, bedfile, do.blind.QC = FALSE, ncores = 2)
str(df_rel)
library(ggplot2)
qplot(Z0, Z1, data = df_rel, col = RT)
qplot(y = PI_HAT, data = df_rel) +
geom_hline(yintercept = 0.2, color = "blue", linetype = 2)
snp_plinkRmSamples(plink, bedfile,
bedfile.out = tempfile(fileext = ".bed"),
df.or.files = subset(df_rel, PI_HAT > 0.2))
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.