seqSetFilterCond: Set a Filter to Variant with Allele Count/Freq

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

Set a Filter to Variant with Allele Count/Freq

Description

Sets a filter to variant with specified allele count/frequency and missing rate.

Usage

seqSetFilterCond(gdsfile, maf=NaN, mac=1L, missing.rate=NaN,
    parallel=seqGetParallel(), .progress=FALSE, verbose=TRUE)

Arguments

gdsfile	a SeqVarGDSClass object
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
.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.
verbose	if TRUE, show information

Value

None.

Author(s)

Xiuwen Zheng

See Also

seqSetFilter, seqSetFilterChrom, seqAlleleFreq, seqAlleleCount, seqMissing

Examples

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

# display
(f <- seqOpen(gds.fn))

seqSetFilterChrom(f, c(1, 6))
seqSetFilterCond(f, maf=0.05, .progress=TRUE)

seqSetFilterChrom(f, c(1, 6))
seqSetFilterCond(f, maf=c(0.01, 0.05), .progress=TRUE)



# close the GDS file
seqClose(f)

zhengxwen/SeqArray documentation built on Nov. 19, 2024, 1:04 p.m.