seqSetFilterCond {SeqArray} | R Documentation

## 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)

[Package SeqArray version 1.28.1 Index]