SeqArray (version 1.8.0)

seqGetFilter: Get the Filter of Samples and Variants

Description

Get the filter of samples and variants

Usage

seqGetFilter(gdsfile)

Arguments

gdsfile

a SeqVarGDSClass object

Value

Return a list:

sample.sel

a logical vector for selected samples

variant.sel

a logical vector for selected variants

Details

It is strongly suggested to call seqOpen instead of openfn.gds, since seqOpen will initialize the internal data for seqGetData, seqApply, etc.

See Also

seqGetData, seqApply

Examples

# the file of GDS
gds.fn <- seqExampleFileName("gds")
# or gds.fn <- "C:/YourFolder/Your_GDS_File.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"))


# 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 filter
z <- seqGetFilter(f)

# the number of selected samples
sum(z$sample.sel)
# the number of selected variants
sum(z$variant.sel)


# close the GDS file
seqClose(f)