snpgdsPairScore: Genotype Score for Pairs of Individuals

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

Description

Calculate the genotype score for pairs of individuals based on identity-by-state (IBS) measure

Usage

snpgdsPairScore(gdsobj, sample1.id, sample2.id, snp.id=NULL,
    method=c("IBS", "GVH", "HVG", "GVH.major", "GVH.minor", "GVH.major.only",
    "GVH.minor.only"), type=c("per.pair", "per.snp", "matrix", "gds.file"),
    dosage=TRUE, with.id=TRUE, output=NULL, verbose=TRUE)

Arguments

gdsobj	an object of class SNPGDSFileClass, a SNP GDS file
sample1.id	a vector of sample id specifying selected samples; if NULL, all samples are used
sample2.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
method	"IBS" – identity-by-state score, "GVH" or "HVG", see Details
type	"per.pair", "per.snp" or "matrix", see Value
dosage	TRUE, uses dosages 0, 1, 2; FALSE, uses 0, 1 (changing a return value of 1 or 2 to be 1)
with.id	if TRUE, returns "sample.id" and "snp.id"; see Value
output	if type="gds.file", the file name
verbose	if TRUE, show information

Details

sample1.id	sample2.id
Patient	Donor	IBS	GVH	HVG	GVH.major	GVH.minor	GVH.major.only	GVH.minor.only
AA / 2	AA / 2	2	0	0	0	0	0	0
AA / 2	AB / 1	1	0	1	0	0	0	0
AA / 2	BB / 0	0	2	2	1	0	1	NA
AB / 1	AA / 2	1	1	0	0	1	NA	1
AB / 1	AB / 1	2	0	0	0	0	0	0
AB / 1	BB / 0	1	1	0	1	0	1	NA
BB / 0	AA / 2	0	2	2	0	1	NA	1
BB / 0	AB / 1	1	0	1	0	0	0	0
BB / 0	BB / 0	2	0	0	0	0	0	0

Value

Return a list:

sample.id	the sample ids used in the analysis, if with.id=TRUE
snp.id	the SNP ids used in the analysis, if with.id=TRUE
score	a matrix of genotype score: if type="per.pair", a data.frame with the first column for average scores, the second column for standard deviation and the third column for the valid number of SNPs; the additional columns for pairs of samples. if type="per.snp", a 3-by-# of SNPs matrix with the first row for average scores, the second row for standard deviation and the third row for the valid number of individual pairs; if type="matrix", a # of pairs-by-# of SNPs matrix with rows for pairs of individuals

Author(s)

Xiuwen Zheng

References

Warren, E. H., Zhang, X. C., Li, S., Fan, W., Storer, B. E., Chien, J. W., Boeckh, M. J., et al. (2012). Effect of MHC and non-MHC donor/recipient genetic disparity on the outcome of allogeneic HCT. Blood, 120(14), 2796-806. doi:10.1182/blood-2012-04-347286

See Also

snpgdsIBS

Examples

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

# autosomal SNPs
selsnp <- snpgdsSelectSNP(genofile, autosome.only=TRUE, remove.monosnp=FALSE)

# sample ID
sample.id <- read.gdsn(index.gdsn(genofile, "sample.id"))
father.id <- read.gdsn(index.gdsn(genofile, "sample.annot/father.id"))

offspring.id <- sample.id[father.id != ""]
father.id <- father.id[father.id != ""]


# calculate average genotype scores
z1 <- snpgdsPairScore(genofile, offspring.id, father.id, snp.id=selsnp,
    method="IBS", type="per.pair")
str(z1)
head(z1$score)

# calculate average genotype scores
z1 <- snpgdsPairScore(genofile, offspring.id, father.id, snp.id=selsnp,
    method="IBS", type="per.pair", dosage=FALSE)
str(z1)
head(z1$score)


# calculate average genotype scores
z2 <- snpgdsPairScore(genofile, offspring.id, father.id, snp.id=selsnp,
    method="IBS", type="per.snp")
str(z2)
z2$score[, 1:4]
mean(z2$score["Avg",])
mean(z2$score["SD",])

plot(z2$score["Avg",], pch=20, cex=0.75, xlab="SNP Index", ylab="IBS score")


# calculate a matrix of genotype scores over samples and SNPs
z3 <- snpgdsPairScore(genofile, offspring.id, father.id, snp.id=selsnp,
    method="IBS", type="matrix")
str(z3)


# output the score matrix to a GDS file
snpgdsPairScore(genofile, offspring.id, father.id, snp.id=selsnp,
    method="IBS", type="gds.file", output="tmp.gds")
(f <- snpgdsOpen("tmp.gds"))
snpgdsClose(f)


# close the file
snpgdsClose(genofile)

unlink("tmp.gds", force=TRUE)

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