seqAlleleFreq {SeqArray}

R Documentation

Get Allele Frequencies or Counts

Description

Calculates the allele frequencies or counts for reference or minor alleles.

Usage

seqAlleleFreq(gdsfile, ref.allele=0L, minor=FALSE, .progress=FALSE,
    parallel=seqGetParallel(), verbose=FALSE)
seqAlleleCount(gdsfile, ref.allele=0L, minor=FALSE, .progress=FALSE,
    parallel=seqGetParallel(), verbose=FALSE)

Arguments

gdsfile	a SeqVarGDSClass object
ref.allele	NULL, a single numeric value, a numeric vector or a character vector; see Value
minor	if TRUE, return minor allele frequency/count
.progress	[deprecated] if TRUE, show progress information
parallel	FALSE (serial processing), TRUE (multicore processing), numeric value or other value; parallel is passed to the argument cl in seqParallel, see seqParallel for more details.
verbose	if TRUE, show progress information

Details

If the gds node 'genotype/data' (integer genotypes) is not available, the node 'annotation/format/DS' (numeric genotype dosages for alternative alleles) will be used to calculate allele frequencies. At a site, it assumes 'annotation/format/DS' stores the dosage of the 1st alternative allele in the 1st column, 2nd alt. allele in the 2nd column if it is multi-allelic, and so on.

Value

If ref.allele=NULL, the function returns a list of allele frequencies/counts according to all allele per site. If ref.allele is a single numeric value (like 0L), it returns a numeric/integer vector for the specified allele (0L for the reference allele, 1L for the first alternative allele, etc). If ref.allele is a numeric vector, ref.allele specifies each allele per site. If ref.allele is a character vector, ref.allele specifies the desired allele for each site (e.g, ancestral allele for the derived allele frequency/count).

Author(s)

Xiuwen Zheng

See Also

seqNumAllele, seqMissing, seqParallel, seqGetParallel

Examples

# the GDS file
(gds.fn <- seqExampleFileName("gds"))

# display
f <- seqOpen(gds.fn)

# return a list
head(seqAlleleFreq(f, NULL, verbose=TRUE))

# return a numeric vector
summary(seqAlleleFreq(f, 0L, verbose=TRUE))

# return a numeric vector
summary(seqAlleleFreq(f, 0L, minor=TRUE, verbose=TRUE))

# return a numeric vector, AA is ancestral allele
AA <- seqGetData(f, "annotation/info/AA", .padNA=TRUE)
summary(seqAlleleFreq(f, AA))
summary(seqAlleleFreq(f, AA, minor=TRUE))

# allele counts
head(seqAlleleCount(f, NULL, verbose=TRUE))
head(seqAlleleCount(f, 0L, verbose=TRUE))
head(seqAlleleCount(f, 0L, minor=TRUE, verbose=TRUE))
head(seqAlleleCount(f, AA, verbose=TRUE))
head(seqAlleleCount(f, AA, minor=TRUE, verbose=TRUE))

# close the GDS file
seqClose(f)

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