SeqArray (version 1.10.1)

seqSetFilter-methods: Set a Filter to Sample or Variant

Description

Sets a filter to sample and/or variant.

Usage

"seqSetFilter"(object, sample.id=NULL, variant.id=NULL, samp.sel=NULL, variant.sel=NULL, action=c("set", "intersect", "push", "push+set", "push+intersect", "pop"), verbose=TRUE)
seqResetFilter(object, sample=TRUE, variant=TRUE, verbose=TRUE)

Arguments

object

a SeqVarGDSClass object

sample.id

IDs of selected samples

variant.id

IDs of selected variants

samp.sel

a logical/raw vector indicating the selected samples

variant.sel

a logical/raw vector indicating the selected variants

action

"set" -- set the current filter via sample.id, variant.id, samp.sel or variant.sel; "intersect" -- set the current filter to the intersection of selected samples and/or variants; "push" -- push the current filter to the stack, and it could be recovered by "pop" later, no change on the current filter; "push+set" -- push the current filter to the stack, and changes the current filter via sample.id, variant.id, samp.sel or variant.sel; "push+intersect" -- push the current filter to the stack, and set the current filter to the intersection of selected samples and/or variants; "pop" -- pop up the last filter

sample

logical, if TRUE, include all samples

variant

logical, if TRUE, include all variants

verbose

if TRUE, show information

Value

None.

Details

seqResetFilter(file) is equivalent to seqSetFilter(file), where the selection arguments in seqSetFilter are NULL.

See Also

seqGetFilter, seqSetFilterChrom, seqGetData, seqApply

Examples

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

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

# get 'sample.id
(samp.id <- seqGetData(f, "sample.id"))
# "NA06984" "NA06985" "NA06986" ...

# get 'variant.id'
head(variant.id <- seqGetData(f, "variant.id"))

# get 'chromosome'
table(seqGetData(f, "chromosome"))

# get 'allele'
head(seqGetData(f, "allele"))
# "T,C" "G,A" "G,A" ...


# set sample and variant filters
seqSetFilter(f, sample.id=samp.id[c(2,4,6,8,10)])
set.seed(100)
seqSetFilter(f, variant.id=sample(variant.id, 10))

# get genotypic data
seqGetData(f, "genotype")



## set the intersection

seqResetFilter(f)
seqSetFilterChrom(f, 10L)
seqSummary(f, "genotype", check="none")

AF <- seqAlleleFreq(f)
table(AF <= 0.9)

seqSetFilter(f, variant.sel=(AF<=0.9), action="intersect")
seqSummary(f, "genotype", check="none")


# close the GDS file
seqClose(f)