Iterator-class: Iterators

In SeqVarTools: Tools for variant data

Description

Extends SeqVarData to provide iterators over variants.

Details

Iterator classes allow for iterating filters over blocks of variants, ranges, or sliding windows.

For SeqVarBlockIterator, each call to iterateFilter will select the next unit of variantBlock variants.

For SeqVarRangeIterator, each call to iterateFilter will select the next range in variantRanges.

SeqVarWindowIterator is an extension of SeqVarRangeIterator where the ranges are determined automatically by sliding a window of size windowSize base pairs by steps of windowShift across the genome. Only windows containing unique sets of variants are kept.

For SeqVarListIterator, each call to iterateFilter will select the next set of ranges in variantRanges.

Any filter set on the object previously will be applied in addition to the selected blocks or ranges.

Constructors

SeqVarBlockIterator(seqData, variantBlock=10000, verbose=TRUE): Returns a SeqVarBlockIterator object with the filter set to the first block.

seqData is a SeqVarData object.

variantBlock is an integer specifying the number of variants in an iteration block.

verbose is a logical indicator for verbose output.

SeqVarRangeIterator(seqData, variantRanges=GRanges(), verbose=TRUE): Returns a SeqVarRangeIterator object with the filter set to the first range.

seqData is a SeqVarData object.

variantRanges is a GRanges object specifying the ranges for iteration.

verbose is a logical indicator for verbose output.

SeqVarWindowIterator(seqData, windowSize=10000, windowShift=5000, verbose=TRUE): Returns a SeqVarWindowIterator object with the filter set to the first window.

seqData is a SeqVarData object.

windowSize is the size in base pairs of the sliding window.

windowShift is the size in base pairs of the step for each consecutive window.

verbose is a logical indicator for verbose output.

SeqVarListIterator(seqData, variantRanges, verbose=TRUE): Returns a SeqVarRangeIterator object with the filter set to the first range.

seqData is a SeqVarData object.

variantRanges is a GRangesList object specifying the ranges for iteration.

verbose is a logical indicator for verbose output.

Accessors

iterateFilter(x): Advance the filter to the next block, range, or set of ranges. Returns TRUE while there are still variants left to be read, FALSE if the end of iteration is reached.

lastFilter(x), lastFilter(x)<- value: Get or set the last filter index from the previous call to iterateFilter.

variantBlock(x): Get the size of the variant block.

variantFilter(x): Get the list of variant indices.

variantRanges(x): Get the variant ranges.

currentRanges(x): Get the ranges selected in the current iteration.

currentVariants(x): Get the variants selected in the current iteration. Returns a DataFrame where the row name is the variant.id, "variant" is the variant position as a link{GRanges}, "range" is the range the variant is from, and any columns in either variantData or the metadata columns of currentRanges are included.

resetIterator(x): Set the filter to the first block, range, or set of ranges (the same variants that are selected when the iterator object is created).

Author(s)

Stephanie Gogarten

See Also

SeqVarGDSClass, SeqVarData, seqSetFilter

Examples

gds <- seqOpen(seqExampleFileName("gds"))
seqData <- SeqVarData(gds)

# iterate by blocks
seqSetFilter(seqData, variant.sel=seq(1,1000,2))
iterator <- SeqVarBlockIterator(seqData, variantBlock=10)
seqGetData(iterator, "variant.id")
iterateFilter(iterator)
seqGetData(iterator, "variant.id")
seqResetFilter(iterator)

# iterate by ranges
library(GenomicRanges)
gr <- GRanges(seqnames=rep(1,3), ranges=IRanges(start=c(1e6, 2e6, 3e6), width=1e6))
iterator <- SeqVarRangeIterator(seqData, variantRanges=gr)
granges(iterator)
iterateFilter(iterator) # no variants in the second range
granges(iterator)
iterateFilter(iterator)
granges(iterator)
iterateFilter(iterator)
seqResetFilter(iterator)

# iterate by windows
seqSetFilterChrom(seqData, include="22")
iterator <- SeqVarWindowIterator(seqData)
seqGetData(iterator, "variant.id")
while (iterateFilter(iterator)) {
    print(seqGetData(iterator, "variant.id"))
}
seqResetFilter(iterator)

# iterate by list of ranges
gr <- GRangesList(
  GRanges(seqnames=rep(22,2), ranges=IRanges(start=c(16e6, 17e6), width=1e6)),
  GRanges(seqnames=rep(22,2), ranges=IRanges(start=c(18e6, 20e6), width=1e6)))
iterator <- SeqVarListIterator(seqData, variantRanges=gr)
granges(iterator)
iterateFilter(iterator)
granges(iterator)
iterateFilter(iterator)
resetIterator(iterator)

seqClose(iterator)

SeqVarTools documentation built on Nov. 22, 2020, 2 a.m.