or relatedness

admixMap

R Documentation

admixMap

Description

Run admixture analyses

Usage

admixMap(admixDataList, null.model, male.diploid=TRUE,
         genome.build=c("hg19", "hg38"),
         BPPARAM=bpparam(), verbose=TRUE)

Arguments

`admixDataList`	named list of `GenotypeIterator` or `SeqVarIterator` objects for each ancestry
`null.model`	A null model object returned by `fitNullModel`.
`male.diploid`	Logical for whether males on sex chromosomes are coded as diploid. Default is 'male.diploid=TRUE', meaning sex chromosome genotypes for males have values 0/2. If the input object codes males as 0/1 on sex chromosomes, set 'male.diploid=FALSE'.
`genome.build`	A character sting indicating genome build; used to identify pseudoautosomal regions on the X and Y chromosomes. These regions are not treated as sex chromosomes when calculating allele frequencies.
`BPPARAM`	A `BiocParallelParam` object to process blocks of variants in parallel. If not provided, the default back-end returned by `bpparam` will be used.
`verbose`	Logical indicator of whether updates from the function should be printed to the console; the default is TRUE.

Details

This function is used with local ancestry results such as those obtained from RFMix. RFMix output may be converted to PLINK format, and then to GDS with snpgdsBED2GDS.

admixDataList should have one value for each ancestry to be included in the test. The sum of all local ancestries at a particular locus must add up to 2, so if there are K ancestry groups, then only K-1 genotypes can be included since one local ancestry count can be written as a linear combination of all of the other local ancestry counts, resulting in collinearity and a matrix that won't be invertible.

See the example for how one might set up the admixDataList object. List names will propagate to the output file.

admixMap uses the BiocParallel package to process iterator chunks in parallel. See the BiocParallel documentation for more information on the default behaviour of bpparam and how to register different parallel backends. If serial execution is desired, set BPPARAM=BiocParallel::SerialParam(). Note that parallel execution requires more RAM than serial execution.

p-values that are calculated using pchisq and are smaller than .Machine\$double.xmin are set to .Machine\$double.xmin.

Value

A data.frame where each row refers to a different variant with the columns:

`variant.id`	The variant ID
`chr`	The chromosome value
`pos`	The base pair position
`n.obs`	The number of samples with non-missing genotypes
`*.freq`	The estimated frequency of alleles derived from each ancestry at that variant
`*.Est`	The effect size estimate for each additional copy of an allele derived from each ancestry, relative to the reference ancestry
`*.SE`	The estimated standard error of the effect size estimate for each ancestry
`Joint.Stat`	The chi-square Wald test statistic for the joint test of all local ancestry terms
`Joint.pval`	The Wald p-value for the joint test of all local ancestry terms

Author(s)

Matthew P. Conomos, Lisa Brown, Stephanie M. Gogarten, Tamar Sofer, Ken Rice, Chaoyu Yu

References

Brown, L.A. et al. (2017). Admixture Mapping Identifies an Amerindian Ancestry Locus Associated with Albuminuria in Hispanics in the United States. J Am Soc Nephrol. 28(7):2211-2220.

Maples, B.K. et al. (2013). RFMix: a discriminative modeling approach for rapid and robust local-ancestry inference. Am J Hum Genet. 93(2):278-88.

Examples

library(GWASTools)

# option 1: one GDS file per ancestry
afrfile <- system.file("extdata", "HapMap_ASW_MXL_local_afr.gds", package="GENESIS")
amerfile <- system.file("extdata", "HapMap_ASW_MXL_local_amer.gds", package="GENESIS")
eurfile <- system.file("extdata", "HapMap_ASW_MXL_local_eur.gds", package="GENESIS")
files <- list(afr=afrfile, amer=amerfile, eur=eurfile)
gdsList <- lapply(files, GdsGenotypeReader)

# make ScanAnnotationDataFrame
scanAnnot <- ScanAnnotationDataFrame(data.frame(
    scanID=getScanID(gdsList[[1]]), stringsAsFactors=FALSE))

# generate a phenotype
set.seed(4)
nsamp <- nrow(scanAnnot)
scanAnnot$pheno <- rnorm(nsamp, mean=0, sd=1)
set.seed(5)
scanAnnot$covar <- sample(0:1, nsamp, replace=TRUE)

genoDataList <- lapply(gdsList, GenotypeData, scanAnnot=scanAnnot)

# iterators
# if we have 3 ancestries total, only 2 should be included in test
genoIterators <- lapply(genoDataList[1:2], GenotypeBlockIterator)

# fit the null mixed model
null.model <- fitNullModel(scanAnnot, outcome="pheno", covars="covar")

# run the association test
myassoc <- admixMap(genoIterators, null.model,
                    BPPARAM=BiocParallel::SerialParam())
head(myassoc)

lapply(genoDataList, close)


# option 2: create a single file with multiple ancestries
# first, get dosages from all ancestries
library(gdsfmt)
dosages <- lapply(files, function(f) {
    gds <- openfn.gds(f)
    geno <- read.gdsn(index.gdsn(gds, "genotype"))
    closefn.gds(gds)
    geno
})
lapply(dosages, dim)

# create a new file with three dosage matrices, keeping all
# sample and snp nodes from one original file
tmpfile <- tempfile()
file.copy(afrfile, tmpfile)
gds <- openfn.gds(tmpfile, readonly=FALSE)
delete.gdsn(index.gdsn(gds, "genotype"))
add.gdsn(gds, "dosage_afr", dosages[["afr"]])
add.gdsn(gds, "dosage_amer", dosages[["amer"]])
add.gdsn(gds, "dosage_eur", dosages[["eur"]])
closefn.gds(gds)
cleanup.gds(tmpfile)

# read in GDS data, specifying the node for each ancestry
gds <- openfn.gds(tmpfile)
gds
genoDataList <- list()
for (anc in c("afr", "amer", "eur")){
  gdsr <- GdsGenotypeReader(gds, genotypeVar=paste0("dosage_", anc))
  genoDataList[[anc]] <- GenotypeData(gdsr, scanAnnot=scanAnnot)
}

# iterators
genoIterators <- lapply(genoDataList[1:2], GenotypeBlockIterator)

# run the association test
myassoc <- admixMap(genoIterators, null.model,
                    BPPARAM=BiocParallel::SerialParam())

close(genoDataList[[1]])
unlink(tmpfile)

UW-GAC/GENESIS documentation built on March 30, 2024, 11:28 p.m.