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Usually, C+T users assign default values for clumping, such as r c 2 of 0.1 (default of PRSice), 0.2 or 0.5 (default of PLINK), and w c of 250 kb (default of PRSice and PLINK) or 500 kb, and test several values for p T ranging from 1 to 10 −8. 2, 4, 5, 7 Moreover, to compute the PRS, the target sample genotypes are usually imputed to some.
PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. We identified 74,274,427 single nucleotide polymorphisms (SNPs) and 13,607,850 insertion-deletions (InDels) by aligning these sequences to the latest version of the goat reference genome (ARS1). A Neighbor-joining tree based on Reynolds genetic ...
plink --bfile mydata -- recode --out mynewdata You might also want to use the variant --recode12 and --recodeAD forms, described here. To speed up input of a large fileset As well as using the binary fileformat, which greatly increases speed of loading relative to the PED/MAP format, if you know that you have already excluded all the individuals you want (with the per-individual.
LD clumping Description. For a bigSNP: snp_pruning(): LD pruning. Similar to "--indep-pairwise (size+1) 1 thr.r2" in PLINK. This function is deprecated (see this article). snp_clumping() (and bed_clumping()): LD clumping. If you do not provide any statistic to rank SNPs, it would use minor allele frequencies (MAFs), making clumping ...
Using the command line Viewing output files Version history 4. Command reference table List of options List of output files Under development 5. Basic usage/data formats Running PLINK PED files MAP files Transposed filesets Long-format filesets Binary PED files Alternate phenotypes Covariate files Cluster files Set files 6. Data management Recode
Usually, C+T users assign default values for clumping, such as r c 2 of 0.1 (default of PRSice), 0.2 or 0.5 (default of PLINK), and w c of 250 kb (default of PRSice and PLINK) or 500 kb, and test several values for p T ranging from 1 to 10 −8. 2, 4, 5, 7 Moreover, to compute the PRS, the target sample genotypes are usually imputed to some ...