seqUnitFilterCond: Filter unit variants

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

Filter unit variants

Description

Filters out the unit variants according to MAF, MAC and missing rates.

Usage

seqUnitFilterCond(gdsfile, units, maf=NaN, mac=1L, missing.rate=NaN,
    minsize=1L, parallel=seqGetParallel(), verbose=TRUE)

Arguments

gdsfile	a SeqVarGDSClass object
units	a list of units of selected variants, with S3 class SeqUnitListClass
maf	minimum minor reference allele frequency, or a range of MAF maf[1] <= ... < maf[2]
mac	minimum minor reference allele count, or a range of MAC mac[1] <= ... < mac[2]
missing.rate	maximum missing genotype rate
minsize	the minimum of unit size
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 information

Value

A S3 object with the class name "SeqUnitListClass" and two components (desp and index): the first is a data.frame with columns "chr", "start" and "end", and the second is list of integer vectors (the variant indices).

Author(s)

Xiuwen Zheng

See Also

seqUnitApply, seqUnitCreate, seqUnitSubset, seqUnitMerge

Examples

# open the GDS file
gdsfile <- seqOpen(seqExampleFileName("gds"))

unit1 <- seqUnitSlidingWindows(gdsfile)
unit1 # "desp"  "index"

# only rare variants
newunit <- seqUnitFilterCond(gdsfile, unit1, maf=c(0, 0.01))
newunit


# excluded variants
exvar <- setdiff(unique(unlist(unit1$index)), unique(unlist(newunit$index)))

seqSetFilter(gdsfile, variant.sel=exvar)
maf <- seqAlleleFreq(gdsfile, minor=TRUE)
table(maf > 0)
summary(maf[maf > 0])  # > 0.01


# close the GDS file
seqClose(gdsfile)

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