seqAlleleFreq {SeqArray} | R Documentation |
Calculates the allele frequencies or counts.
seqAlleleFreq(gdsfile, ref.allele=0L, .progress=FALSE, parallel=seqGetParallel()) seqAlleleCount(gdsfile, ref.allele=0L, .progress=FALSE, parallel=seqGetParallel())
gdsfile |
a |
ref.allele |
|
.progress |
if |
parallel |
|
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).
Xiuwen Zheng
seqNumAllele
, seqMissing
,
seqParallel
, seqGetParallel
# 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)