snpgdsMergeGRM {SNPRelate} | R Documentation

## Merge Multiple Genetic Relationship Matrices (GRM)

### Description

Combine multiple genetic relationship matrices with weighted averaging.

### Usage

    snpgdsMergeGRM(filelist, out.fn=NULL, out.prec=c("double", "single"),
        out.compress="LZMA_RA", weight=NULL, verbose=TRUE)

### Arguments

`filelist` | a character vector, list of GDS file names
`out.fn` | NULL, return a GRM object; or characters, the output GDS file name
`out.prec` | double or single precision for storage
`out.compress` | the compression method for storing the GRM matrix in the GDS file
`weight` | NULL, weights proportional to the numbers of SNPs; a numeric vector, or a logical vector (FALSE for excluding some GRMs with a negative weight, weights proportional to the numbers of SNPs)
`verbose` | if `TRUE`, show information

### Details

The final GRM is the weighted averaged matrix combining multiple GRMs. The merged GRM may not be identical to the GRM calculated using full SNPs, due to missing genotypes or the internal weighting strategy of the specified GRM calculation.

### Value

None or a GRM object if `out.fn=NULL`.

### Author(s)

Xiuwen Zheng

### See Also

`snpgdsGRM`

### Examples

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

    snpid <- read.gdsn(index.gdsn(genofile, "snp.id"))
    snpid <- snpid[snpgdsSNPRateFreq(genofile)$MissingRate == 0]

    # there is no missing genotype
    grm <- snpgdsGRM(genofile, snp.id=snpid, method="GCTA")

    # save two GRMs
    set1 <- grm$snp.id[1:(length(grm$snp.id)/2)]
    set2 <- setdiff(grm$snp.id, set1)
    snpgdsGRM(genofile, method="GCTA", snp.id=set1, out.fn="tmp1.gds")
    snpgdsGRM(genofile, method="GCTA", snp.id=set2, out.fn="tmp2.gds")

    # merge GRMs and export to a new GDS file
    snpgdsMergeGRM(c("tmp1.gds", "tmp2.gds"), "tmp.gds")

    # return the GRM
    grm2 <- snpgdsMergeGRM(c("tmp1.gds", "tmp2.gds"))

    # check
    f <- openfn.gds("tmp.gds")
    m <- read.gdsn(index.gdsn(f, "grm"))
    closefn.gds(f)

    summary(c(m - grm$grm))  # ~zero
    summary(c(m - grm2$grm))  # zero

    # close the file
    snpgdsClose(genofile)

    # delete the temporary file
    unlink(c("tmp1.gds", "tmp2.gds", "tmp.gds"), force=TRUE)

[Package SNPRelate version 1.20.1 Index]