seqSetFilter: Set a Filter to Sample or Variant

In SeqArray: Data management of large-scale whole-genome sequence variant calls

Description

Sets a filter to sample and/or variant.

Usage

## S4 method for signature 'SeqVarGDSClass,ANY'
seqSetFilter(object, variant.sel,
    sample.sel=NULL, variant.id=NULL, sample.id=NULL,
    action=c("set", "intersect", "push", "push+set", "push+intersect", "pop"),
    verbose=TRUE)
## S4 method for signature 'SeqVarGDSClass,GRanges'
seqSetFilter(object, variant.sel,
    rm.txt="chr", intersect=FALSE, verbose=TRUE)
## S4 method for signature 'SeqVarGDSClass,GRangesList'
seqSetFilter(object, variant.sel,
    rm.txt="chr", intersect=FALSE, verbose=TRUE)
## S4 method for signature 'SeqVarGDSClass,IRanges'
seqSetFilter(object, variant.sel,
    chr, intersect=FALSE, verbose=TRUE)
seqResetFilter(object, sample=TRUE, variant=TRUE, verbose=TRUE)
seqSetFilterChrom(object, include=NULL, is.num=NA, from.bp=NULL, to.bp=NULL,
    intersect=FALSE, verbose=TRUE)
seqSetFilterPos(object, chr, pos, intersect=FALSE, multi.pos=FALSE,
    verbose=TRUE)
seqSetFilterAnnotID(object, id, verbose=TRUE)

Arguments

object	a SeqVarGDSClass object
variant.sel	a logical/raw/index vector indicating the selected variants; GRanges, a GRanges object for the genomic locations; GRangesList, a GRangesList object for storing a collection of GRanges objects; IRanges, a IRanges object for storing a collection of range objects
sample.sel	a logical/raw/index vector indicating the selected samples
variant.id	ID of selected variants
sample.id	ID of selected samples
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
rm.txt	a character, the characters will be removed from seqnames(variant.sel)
chr	a vector of character for chromsome coding
pos	a vector of numeric values for genome coordinate
sample	logical, if TRUE, include all samples
variant	logical, if TRUE, include all variants
include	NULL, or a vector of characters for specified chromosome(s)
is.num	a logical variable: TRUE, chromosome code is numeric; FALSE, chromosome is not numeric; is.num=TRUE is usually used to exclude non-autosomes
from.bp	NULL, no limit; a numeric vector, the lower bound of position
to.bp	NULL, no limit; a numeric vector, the upper bound of position
intersect	if FALSE, the candidate samples/variants for selection are all samples/variants (by default); if TRUE, the candidate samples/variants are from the selected samples/variants defined via the previous call
multi.pos	FALSE, use the first matched position; TRUE, allow multiple variants at the same position
id	a character vector for RS IDs (stored in "annotation/id")
verbose	if TRUE, show information

Details

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

If from.bp and to.bp has values, they should be equal-size as include. A trio of include, from.bp and to.bp indicates a region on human genomes. NA in from.bp is treated as 0, and NA in to.bp is treated as the maximum of integer (2^31 - 1).

Value

None.

Author(s)

Xiuwen Zheng

See Also

seqSetFilterChrom, seqSetFilterCond, seqGetFilter, 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)])
set.seed(100)
seqSetFilter(f, variant.id=sample(variant.id, 5))

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


## OR
# set sample and variant filters
seqSetFilter(f, sample.sel=c(2,4,6,8))
set.seed(100)
seqSetFilter(f, variant.sel=sample.int(length(variant.id), 5))

# 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")



## chromosome

seqResetFilter(f)

seqSetFilterChrom(f, is.num=TRUE)
seqSummary(f, "genotype", check="none")

seqSetFilterChrom(f, is.num=FALSE)
seqSummary(f, "genotype", check="none")

seqSetFilterChrom(f, 1:4)
seqSummary(f, "genotype", check="none")
table(seqGetData(f, "chromosome"))

# HLA region
seqSetFilterChrom(f, 6, from.bp=29719561, to.bp=32883508)
seqSummary(f, "genotype", check="none")

# two regions
seqSetFilterChrom(f, c(1, 6), from.bp=c(1000000, 29719561),
    to.bp=c(90000000, 32883508))
seqSummary(f, "genotype", check="none")
seqGetData(f, "chromosome")


## intersection option

seqResetFilter(f)
seqSetFilterChrom(f, 6, from.bp=29719561, to.bp=32883508)  # MHC
seqSetFilterChrom(f, include=6)  # chromosome 6

seqResetFilter(f)
seqSetFilterChrom(f, 6, from.bp=29719561, to.bp=32883508)  # MHC
seqSetFilterChrom(f, include=6, intersect=TRUE)  # MHC region only



# close the GDS file
seqClose(f)

SeqArray documentation built on Nov. 8, 2020, 5:08 p.m.