seqSetFilter: Set a Filter to Sample or Variant

In zhengxwen/SeqArray: Data Management of Large-Scale Whole-Genome Sequence Variant Calls

Set a Filter to Sample or Variant

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"),
    ret.idx=FALSE, warn=TRUE, 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, ref=NULL, alt=NULL, intersect=FALSE,
    multi.pos=TRUE, ret.idx=FALSE, verbose=TRUE)
seqSetFilterAnnotID(object, id, ret.idx=FALSE, verbose=TRUE)
seqFilterPush(object)  # store the current filter
seqFilterPop(object)   # restore the last filter

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
ret.idx	if TRUE, return the index in the output array according to the order of 'sample.id', 'sample.sel', 'variant.id' or 'variant.sel'
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
ref	the reference alleles
alt	the alternative alleles
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")
warn	if TRUE, show a warning when the input sample.sel or variant.sel is not ordered as the GDS file or there is any duplicate
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

If ret.idx=TRUE, seqSetFilter() returns a list with two components sample_idx and variant_idx to indicate the indices of the output array according to the input 'sample.id', 'sample.sel', 'variant.id' or 'variant.sel'; if ret.idx=TRUE, seqSetFilterAnnotID() return an index vector; otherwise no return.

Author(s)

Xiuwen Zheng

See Also

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 filters
seqSetFilter(f, sample.id=samp.id[c(2,4,6,8)])
seqSetFilter(f, sample.id=samp.id[c(2,4,6,8)], ret.idx=TRUE)

(v <- seqSetFilter(f, sample.id=samp.id[c(8,2,6,4)], ret.idx=TRUE))
all(seqGetData(f, "sample.id")[v$sample_idx] == samp.id[c(8,2,6,4)])

# set variant filters
seqSetFilter(f, variant.id=variant.id[c(2,4,6,8,10,12)], ret.idx=TRUE)
(v <- seqSetFilter(f, variant.id=variant.id[c(12,4,6,10,8,12)], ret.idx=TRUE))
all(variant.id[c(12,4,6,10,8,12)] == seqGetData(f, "variant.id")[v$variant_idx])

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)

zhengxwen/SeqArray documentation built on Dec. 14, 2024, 8:36 p.m.