snpgdsApartSelection: Select SNPs with a basepair distance

In SNPRelate: Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data

Description

Randomly selects SNPs for which each pair is at least as far apart as the specified basepair distance.

Usage

snpgdsApartSelection(chromosome, position, min.dist=100000,
    max.n.snp.perchr=-1, verbose=TRUE) 

Arguments

chromosome	chromosome codes
position	SNP positions in base pair
min.dist	A numeric value to specify minimum distance required (in basepairs)
max.n.snp.perchr	A numeric value specifying the maximum number of SNPs to return per chromosome, "-1" means no number limit
verbose	if TRUE, show information

Value

A logical vector indicating which SNPs were selected.

Author(s)

Xiuwen Zheng

See Also

snpgdsLDpruning

Examples

# open an example dataset (HapMap)
genofile <- snpgdsOpen(snpgdsExampleFileName())
genofile

chr <- read.gdsn(index.gdsn(genofile, "snp.chromosome"))
pos <- read.gdsn(index.gdsn(genofile, "snp.position"))

set.seed(1000)
flag <- snpgdsApartSelection(chr, pos, min.dist=250000, verbose=TRUE)
table(flag)

# close the genotype file
snpgdsClose(genofile)

Example output

Loading required package: gdsfmt
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
File: /usr/local/lib/R/site-library/SNPRelate/extdata/hapmap_geno.gds (709.6K)
+    [  ] *
|--+ sample.id   { VStr8 279 ZIP(29.9%), 679B }
|--+ snp.id   { Int32 9088 ZIP(34.8%), 12.3K }
|--+ snp.rs.id   { VStr8 9088 ZIP(40.1%), 36.2K }
|--+ snp.position   { Int32 9088 ZIP(94.7%), 33.6K }
|--+ snp.chromosome   { UInt8 9088 ZIP(0.94%), 85B } *
|--+ snp.allele   { VStr8 9088 ZIP(11.3%), 4.0K }
|--+ genotype   { Bit2 279x9088, 619.0K } *
\--+ sample.annot   [ data.frame ] *
   |--+ family.id   { VStr8 279 ZIP(34.4%), 514B }
   |--+ father.id   { VStr8 279 ZIP(31.5%), 220B }
   |--+ mother.id   { VStr8 279 ZIP(30.9%), 214B }
   |--+ sex   { VStr8 279 ZIP(17.0%), 95B }
   \--+ pop.group   { VStr8 279 ZIP(6.18%), 69B }
Thu Jan 17 23:49:13 2019	Chromosome 1, # of SNPs: 365
Thu Jan 17 23:49:13 2019	Chromosome 2, # of SNPs: 370
Thu Jan 17 23:49:13 2019	Chromosome 3, # of SNPs: 314
Thu Jan 17 23:49:13 2019	Chromosome 4, # of SNPs: 294
Thu Jan 17 23:49:13 2019	Chromosome 5, # of SNPs: 291
Thu Jan 17 23:49:13 2019	Chromosome 6, # of SNPs: 280
Thu Jan 17 23:49:13 2019	Chromosome 7, # of SNPs: 245
Thu Jan 17 23:49:13 2019	Chromosome 8, # of SNPs: 232
Thu Jan 17 23:49:13 2019	Chromosome 9, # of SNPs: 203
Thu Jan 17 23:49:13 2019	Chromosome 10, # of SNPs: 224
Thu Jan 17 23:49:13 2019	Chromosome 11, # of SNPs: 227
Thu Jan 17 23:49:13 2019	Chromosome 12, # of SNPs: 215
Thu Jan 17 23:49:13 2019	Chromosome 13, # of SNPs: 175
Thu Jan 17 23:49:13 2019	Chromosome 14, # of SNPs: 147
Thu Jan 17 23:49:13 2019	Chromosome 15, # of SNPs: 127
Thu Jan 17 23:49:13 2019	Chromosome 16, # of SNPs: 128
Thu Jan 17 23:49:13 2019	Chromosome 17, # of SNPs: 112
Thu Jan 17 23:49:13 2019	Chromosome 18, # of SNPs: 127
Thu Jan 17 23:49:13 2019	Chromosome 19, # of SNPs: 76
Thu Jan 17 23:49:13 2019	Chromosome 20, # of SNPs: 107
Thu Jan 17 23:49:13 2019	Chromosome 21, # of SNPs: 63
Thu Jan 17 23:49:13 2019	Chromosome 22, # of SNPs: 54
Thu Jan 17 23:49:13 2019	Chromosome 23, # of SNPs: 215
Total # of SNPs selected:4591
flag
FALSE  TRUE 
 4497  4591 

SNPRelate documentation built on Nov. 8, 2020, 5:31 p.m.