seqSetFilterCond: Set a Filter to Variant with Allele Count/Freq
In SeqArray: Data management of large-scale whole-genome sequence variant calls

Description Usage Arguments Value Author(s) See Also Examples

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

1 2	seqSetFilterCond(gdsfile, maf=NaN, mac=1L, missing.rate=NaN, parallel=seqGetParallel(), .progress=FALSE, verbose=TRUE)

`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

None.

Xiuwen Zheng

seqSetFilter, seqSetFilterChrom, seqAlleleFreq, seqAlleleCount, seqMissing

# 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)