The MatchedGRanges class is a subclass of both
Matched and GRanges. Therefore, it contains slots
and methods for both of these classes.
The MatchedGRanges class uses a delegate object
during initialization to assign its GRanges slots.
MatchedGRanges behaves as a GRanges but also
includes additional Matched object functionality
(see ?Matched). For more information about
GRanges see ?GenomicRanges::GRanges.
focalA GRanges object containing the focal
data to match.
poolA GRanges object containing the pool
from which to select matches.
delegateA GRanges object used to initialize
GRanges-specific slots. matchRanges() assigns
the matched set to the slot.
matchedDataA data.table with matched data
matchedIndexAn integer vector corresponding
to the indices in the pool which comprise the
matched set.
covarA character vector describing the covariates used for matching.
methodCharacter describing replacement method used for matching.
replaceTRUE/FALSE describing if matching was done with or without replacement.
seqnamesseqnames(delegate)
rangesranges(delegate)
strandstrand(delegate)
seqinfoseqinfo(delegate)
elementMetadataelementMetadata(delegate)
elementTypeelementType(delegate)
metadatametadata(delegate)
Functions that get data from Matched subclasses (x)
such as MatchedDataFrame, MatchedGRanges,
and MatchedGInteractions are listed below:
matchedData(x): Get matched data from a Matched object
covariates(x): Get covariates from a Matched object
method(x): Get matching method used for Matched object
withReplacement(x): Get replace method
indices(x, set): Get indices of matched set
For more detail check the help pages for these functions.
Additional functions that get data from Matched subclasses
(x) such as MatchedDataFrame, MatchedGRanges,
and MatchedGInteractions include:
focal(x): Get focal set from a Matched object
pool(x): Get pool set from a Matched object
matched(x): Get matched set from a Matched object
unmatched(x): Get unmatched set from a Matched object
For more detail check the help pages for these functions.
## Contructing MatchedGRanges with matchRanges
set.seed(123)
gr <- makeExampleMatchedDataSet(type = "GRanges")
mgr <- matchRanges(
focal = gr[gr$feature1, ],
pool = gr[!gr$feature1, ],
covar = ~ feature2 + feature3,
method = "rejection",
replace = FALSE
)
class(mgr)
#> [1] "MatchedGRanges"
#> attr(,"package")
#> [1] "nullranges"
## Make MatchedGRanges example
set.seed(123)
x <- makeExampleMatchedDataSet(type = "GRanges", matched = TRUE)
## Accessor functions for Matched class
matchedData(x)
#> id feature2 feature3 ps set
#> 1: 1 2.879049 c 0.21095908 focal
#> 2: 1 3.539645 c 0.19210984 focal
#> 3: 1 7.117417 c 0.11193396 focal
#> 4: 1 4.141017 a 0.01771986 focal
#> 5: 1 4.258575 c 0.17308581 focal
#> ---
#> 20496: 0 1.235781 b 0.08945367 unmatched
#> 20497: 0 1.696712 a 0.02707977 unmatched
#> 20498: 0 6.111404 a 0.01255772 unmatched
#> 20499: 0 2.216575 d 0.07578989 unmatched
#> 20500: 0 5.330029 b 0.04535856 unmatched
covariates(x)
#> [1] "feature2" "feature3"
method(x)
#> [1] "rejection"
withReplacement(x)
#> [1] FALSE
head(indices(x, set = 'matched'))
#> [1] 6100 5198 9886 3619 9077 6763
## Accessor functions for Matched subclasses
focal(x)
#> GRanges object with 500 ranges and 3 metadata columns:
#> seqnames ranges strand | feature1 feature2 feature3
#> <Rle> <IRanges> <Rle> | <logical> <numeric> <character>
#> [1] chr1 1-100 * | TRUE 2.87905 c
#> [2] chr1 2-101 * | TRUE 3.53965 c
#> [3] chr1 3-102 * | TRUE 7.11742 c
#> [4] chr1 4-103 * | TRUE 4.14102 a
#> [5] chr1 5-104 * | TRUE 4.25858 c
#> ... ... ... ... . ... ... ...
#> [496] chr1 496-595 * | TRUE 1.28384 d
#> [497] chr1 497-596 * | TRUE 4.36369 a
#> [498] chr1 498-597 * | TRUE 4.32968 b
#> [499] chr1 499-598 * | TRUE 4.72823 b
#> [500] chr1 500-599 * | TRUE 5.10432 b
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
pool(x)
#> GRanges object with 10000 ranges and 3 metadata columns:
#> seqnames ranges strand | feature1 feature2 feature3
#> <Rle> <IRanges> <Rle> | <logical> <numeric> <character>
#> [1] chr1 501-600 * | FALSE 3.28347 e
#> [2] chr1 502-601 * | FALSE 7.12640 a
#> [3] chr1 503-602 * | FALSE 1.92222 b
#> [4] chr1 504-603 * | FALSE 10.24116 a
#> [5] chr1 505-604 * | FALSE 10.17287 c
#> ... ... ... ... . ... ... ...
#> [9996] chr1 10496-10595 * | FALSE 1.23578 b
#> [9997] chr1 10497-10596 * | FALSE 1.69671 a
#> [9998] chr1 10498-10597 * | FALSE 6.11140 a
#> [9999] chr1 10499-10598 * | FALSE 2.21657 d
#> [10000] chr1 10500-10599 * | FALSE 5.33003 b
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
matched(x)
#> GRanges object with 500 ranges and 3 metadata columns:
#> seqnames ranges strand | feature1 feature2 feature3
#> <Rle> <IRanges> <Rle> | <logical> <numeric> <character>
#> [1] chr1 6600-6699 * | FALSE 2.108420 c
#> [2] chr1 5698-5797 * | FALSE 5.991699 b
#> [3] chr1 10386-10485 * | FALSE 5.696525 b
#> [4] chr1 4119-4218 * | FALSE 0.409923 a
#> [5] chr1 9577-9676 * | FALSE 9.330107 b
#> ... ... ... ... . ... ... ...
#> [496] chr1 1275-1374 * | FALSE 3.27301 b
#> [497] chr1 4976-5075 * | FALSE 8.05522 c
#> [498] chr1 3917-4016 * | FALSE 2.01576 a
#> [499] chr1 10205-10304 * | FALSE 6.60221 b
#> [500] chr1 1841-1940 * | FALSE 7.79926 c
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
unmatched(x)
#> GRanges object with 9500 ranges and 3 metadata columns:
#> seqnames ranges strand | feature1 feature2 feature3
#> <Rle> <IRanges> <Rle> | <logical> <numeric> <character>
#> [1] chr1 501-600 * | FALSE 3.28347 e
#> [2] chr1 502-601 * | FALSE 7.12640 a
#> [3] chr1 503-602 * | FALSE 1.92222 b
#> [4] chr1 504-603 * | FALSE 10.24116 a
#> [5] chr1 505-604 * | FALSE 10.17287 c
#> ... ... ... ... . ... ... ...
#> [9496] chr1 10496-10595 * | FALSE 1.23578 b
#> [9497] chr1 10497-10596 * | FALSE 1.69671 a
#> [9498] chr1 10498-10597 * | FALSE 6.11140 a
#> [9499] chr1 10499-10598 * | FALSE 2.21657 d
#> [9500] chr1 10500-10599 * | FALSE 5.33003 b
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths