seqSetFilter: Set a Filter to Sample or Variant In SeqArray: Data management of large-scale whole-genome sequence variant calls Description Usage Arguments Details Value Author(s) See Also Examples
Description
Sets a filter to sample and/or variant.
Usage
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## 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
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# 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.
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Description Usage Arguments Details Value Author(s) See Also Examples
Description
Sets a filter to sample and/or variant.
Usage
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | ## 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 |
variant.sel | a logical/raw/index vector indicating the selected variants; |
sample.sel | a logical/raw/index vector indicating the selected samples |
variant.id | ID of selected variants |
sample.id | ID of selected samples |
action |
|
rm.txt | a character, the characters will be removed from |
chr | a vector of character for chromsome coding |
pos | a vector of numeric values for genome coordinate |
sample | logical, if |
variant | logical, if |
include | NULL, or a vector of characters for specified chromosome(s) |
is.num | a logical variable: |
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 |
multi.pos |
|
id | a character vector for RS IDs (stored in |
verbose | if |
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 | # 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) |
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