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

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

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)

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