snpgdsPairScore {SNPRelate} | R Documentation

## Genotype Score for Pairs of Individuals

### 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)

[Package SNPRelate version 1.24.0 Index]