an object of class SNPGDSFileClass,
a SNP GDS file
sample.id
a vector of sample id specifying selected samples;
if NULL, all samples are used
snp.id
a vector of snp id specifying selected SNPs; if NULL,
all SNPs are used
autosome.only
if TRUE, use autosomal SNPs only; if it is a
numeric or character value, keep SNPs according to the specified
chromosome
remove.monosnp
if TRUE, remove monomorphic SNPs
maf
to use the SNPs with ">= maf" only; if NaN, no MAF threshold
missing.rate
to use the SNPs with "<= missing.rate" only; if NaN,
no missing threshold
num.thread
the number of (CPU) cores used; if NA, detect
the number of cores automatically
verbose
if TRUE, show information
Details
The minor allele frequency and missing rate for each SNP passed in
snp.id are calculated over all the samples in sample.id.
Value
Return a list (n is the number of samples):
sample.id
the sample ids used in the analysis
snp.id
the SNP ids used in the analysis
ibs0
a n-by-n matrix, the number of SNPs sharing 0 IBS
ibs1
a n-by-n matrix, the number of SNPs sharing 1 IBS
ibs2
a n-by-n matrix, the number of SNPs sharing 2 IBS
Author(s)
Xiuwen Zheng
See Also
snpgdsIBS
Examples
# open an example dataset (HapMap)
genofile <- snpgdsOpen(snpgdsExampleFileName())
RV <- snpgdsIBSNum(genofile)
pop <- read.gdsn(index.gdsn(genofile, "sample.annot/pop.group"))
L <- order(pop)
image(RV$ibs0[L, L]/length(RV$snp.id))
# close the genotype file
snpgdsClose(genofile)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(SNPRelate)
Loading required package: gdsfmt
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/SNPRelate/snpgdsIBSNum.Rd_%03d_medium.png", width=480, height=480)
> ### Name: snpgdsIBSNum
> ### Title: Identity-By-State (IBS)
> ### Aliases: snpgdsIBSNum
> ### Keywords: GDS GWAS
>
> ### ** Examples
>
> # open an example dataset (HapMap)
> genofile <- snpgdsOpen(snpgdsExampleFileName())
>
> RV <- snpgdsIBSNum(genofile)
Identity-By-State (IBS) analysis on SNP genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, < MAF: NaN, or > missing rate: NaN)
Working space: 279 samples, 8722 SNPs
using 1 (CPU) core
IBS: the sum of all selected genotypes (0, 1 and 2) = 2446510
Wed Jul 6 05:34:45 2016 (internal increment: 55808)
[>.................................................] 0%, ETC: NA [==================================================] 100%, completed
Wed Jul 6 05:34:45 2016 Done.
> pop <- read.gdsn(index.gdsn(genofile, "sample.annot/pop.group"))
> L <- order(pop)
> image(RV$ibs0[L, L]/length(RV$snp.id))
>
> # close the genotype file
> snpgdsClose(genofile)
>
>
>
>
>
> dev.off()
null device
1
>