seqAlleleFreq: Get Allele Frequencies or Counts

In zhengxwen/SeqArray: Data Management of Large-Scale Whole-Genome Sequence Variant Calls

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

seqGetAF_AC_Missing() returns data.frame(af, ac, miss) for allele frequencies, allele counts and missing rates. It is faster than calling seqAlleleFreq(), seqAlleleCount() and seqMissing sequentially.

Author(s)

Xiuwen Zheng

See Also

seqMissing, seqNumAllele, 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))

# allele frequencies, allele counts and missing proportions
v <- seqGetAF_AC_Missing(f, minor=TRUE)
head(v)

# close the GDS file
seqClose(f)

zhengxwen/SeqArray documentation built on Dec. 14, 2024, 8:36 p.m.