R: Get Allele Frequencies or Counts

seqAlleleFreq {SeqArray}

R Documentation

Get Allele Frequencies or Counts

Description

Calculates the allele frequencies or counts.

Usage

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

Arguments

`gdsfile`	a `SeqVarGDSClass` object
`ref.allele`	`NULL`, a single numeric value, a numeric vector or a character vector; see Value
`.progress`	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.

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

Examples

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

# display
f <- seqOpen(gds.fn)

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

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

# return a numeric vector, AA is ancestral allele
AA <- toupper(seqGetData(f, "annotation/info/AA")$data)
head(seqAlleleFreq(f, AA))

# allele counts
head(seqAlleleCount(f, NULL, .progress=TRUE))
head(seqAlleleCount(f, 0L, .progress=TRUE))
head(seqAlleleCount(f, AA, .progress=TRUE))

# close the GDS file
seqClose(f)

[Package SeqArray version 1.26.2 Index]