snpgdsSNPRateFreq: Allele Frequency, Minor Allele Frequency, Missing Rate of...

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

Allele Frequency, Minor Allele Frequency, Missing Rate of SNPs

Description

Calculate the allele frequency, minor allele frequency and missing rate per SNP.

Usage

snpgdsSNPRateFreq(gdsobj, sample.id=NULL, snp.id=NULL, with.id=FALSE,
    with.sample.id=FALSE, with.snp.id=FALSE)

Arguments

gdsobj	an object of class SNPGDSFileClass, a SNP GDS file
sample.id	a vector of sample id specifying selected samples; if NULL, all samples will be used
snp.id	a vector of snp id specifying selected SNPs; if NULL, all SNPs will be used
with.id	if TRUE, return both sample and SNP IDs
with.sample.id	if TRUE, return sample IDs
with.snp.id	if TRUE, return SNP IDs

Value

Return a list:

AlleleFreq	allele frequencies
MinorFreq	minor allele frequencies
MissingRate	missing rates
sample.id	sample id, if with.id=TRUE or with.sample.id=TRUE
snp.id	SNP id, if with.id=TRUE or with.snp.id=TRUE

Author(s)

Xiuwen Zheng

See Also

snpgdsSampMissRate

Examples

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

RV <- snpgdsSNPRateFreq(genofile, with.snp.id=TRUE)
head(data.frame(RV))

hist(RV$AlleleFreq, breaks=128)
summary(RV$MissingRate)

# close the file
snpgdsClose(genofile)

zhengxwen/SNPRelate documentation built on April 16, 2024, 8:42 a.m.