seqSetFilterCond {SeqArray} | R Documentation |
Sets a filter to variant with specified allele count/frequency and missing rate.
seqSetFilterCond(gdsfile, maf=NaN, mac=1L, missing.rate=NaN, parallel=seqGetParallel(), .progress=FALSE, verbose=TRUE)
gdsfile |
a |
maf |
minimum minor reference allele frequency, or a range of MAF
|
mac |
minimum minor reference allele count, or a range of MAC
|
missing.rate |
maximum missing genotype rate |
.progress |
if |
parallel |
|
verbose |
if |
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)