MatchedGInteractions objects

Source: R/AllClasses.R

The MatchedGInteractions class is a subclass of both Matched and GInteractions. Therefore, it contains slots and methods for both of these classes.

Details

The MatchedGInteractions class uses a delegate object during initialization to assign its GInteractions slots. MatchedGInteractions behaves as a GInteractions but also includes additional Matched object functionality (see ?Matched). For more information about GInteractions see ?InteractionSet::GInteractions.

Slots

focal

A GInteractions object containing the focal data to match.

pool

A GInteractions object containing the pool from which to select matches.

delegate

A GInteractions object used to initialize GInteractions-specific slots. matchRanges() assigns the matched set to the slot.

matchedData

A data.table with matched data

matchedIndex

An integer vector corresponding to the indices in the pool which comprise the matched set.

covar

A character vector describing the covariates used for matching.

method

Character describing replacement method used for matching.

replace

TRUE/FALSE describing if matching was done with or without replacement.

anchor1

anchorIds(delegate)$first

anchor2

anchorIds(delegate)$second

regions

regions(delegate)

NAMES

names(delegate)

elementMetadata

elementMetadata(delegate)

metadata

metadata(delegate)

Accessor methods for Matched Class

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.

Accessor methods for Matched subclass objects

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.

Examples

## Constructing MatchedGInteractions with matchRanges
set.seed(123)
gi <- makeExampleMatchedDataSet(type = "GInteractions")
mgi <- matchRanges(
  focal = gi[gi$feature1, ],
  pool = gi[!gi$feature1, ],
  covar = ~ feature2 + feature3,
  method = "rejection",
  replace = FALSE
)
class(mgi)
#> [1] "MatchedGInteractions"
#> attr(,"package")
#> [1] "nullranges"

## Make MatchedGInteractions example
set.seed(123)
x <- makeExampleMatchedDataSet(type = "GInteractions", 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)
#> GInteractions object with 500 interactions and 3 metadata columns:
#>         seqnames1   ranges1     seqnames2   ranges2 |  feature1  feature2
#>             <Rle> <IRanges>         <Rle> <IRanges> | <logical> <numeric>
#>     [1]      chr1     1-100 ---      chr1     1-100 |      TRUE   2.87905
#>     [2]      chr1     2-101 ---      chr1     2-101 |      TRUE   3.53965
#>     [3]      chr1     3-102 ---      chr1     3-102 |      TRUE   7.11742
#>     [4]      chr1     4-103 ---      chr1     4-103 |      TRUE   4.14102
#>     [5]      chr1     5-104 ---      chr1     5-104 |      TRUE   4.25858
#>     ...       ...       ... ...       ...       ... .       ...       ...
#>   [496]      chr1   496-595 ---      chr1   496-595 |      TRUE   1.28384
#>   [497]      chr1   497-596 ---      chr1   497-596 |      TRUE   4.36369
#>   [498]      chr1   498-597 ---      chr1   498-597 |      TRUE   4.32968
#>   [499]      chr1   499-598 ---      chr1   499-598 |      TRUE   4.72823
#>   [500]      chr1   500-599 ---      chr1   500-599 |      TRUE   5.10432
#>            feature3
#>         <character>
#>     [1]           c
#>     [2]           c
#>     [3]           c
#>     [4]           a
#>     [5]           c
#>     ...         ...
#>   [496]           d
#>   [497]           a
#>   [498]           b
#>   [499]           b
#>   [500]           b
#>   -------
#>   regions: 10500 ranges and 0 metadata columns
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths
pool(x)
#> GInteractions object with 10000 interactions and 3 metadata columns:
#>           seqnames1     ranges1     seqnames2     ranges2 |  feature1  feature2
#>               <Rle>   <IRanges>         <Rle>   <IRanges> | <logical> <numeric>
#>       [1]      chr1     501-600 ---      chr1     501-600 |     FALSE   3.28347
#>       [2]      chr1     502-601 ---      chr1     502-601 |     FALSE   7.12640
#>       [3]      chr1     503-602 ---      chr1     503-602 |     FALSE   1.92222
#>       [4]      chr1     504-603 ---      chr1     504-603 |     FALSE  10.24116
#>       [5]      chr1     505-604 ---      chr1     505-604 |     FALSE  10.17287
#>       ...       ...         ... ...       ...         ... .       ...       ...
#>    [9996]      chr1 10496-10595 ---      chr1 10496-10595 |     FALSE   1.23578
#>    [9997]      chr1 10497-10596 ---      chr1 10497-10596 |     FALSE   1.69671
#>    [9998]      chr1 10498-10597 ---      chr1 10498-10597 |     FALSE   6.11140
#>    [9999]      chr1 10499-10598 ---      chr1 10499-10598 |     FALSE   2.21657
#>   [10000]      chr1 10500-10599 ---      chr1 10500-10599 |     FALSE   5.33003
#>              feature3
#>           <character>
#>       [1]           e
#>       [2]           a
#>       [3]           b
#>       [4]           a
#>       [5]           c
#>       ...         ...
#>    [9996]           b
#>    [9997]           a
#>    [9998]           a
#>    [9999]           d
#>   [10000]           b
#>   -------
#>   regions: 10500 ranges and 0 metadata columns
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths
matched(x)
#> GInteractions object with 500 interactions and 3 metadata columns:
#>         seqnames1     ranges1     seqnames2     ranges2 |  feature1  feature2
#>             <Rle>   <IRanges>         <Rle>   <IRanges> | <logical> <numeric>
#>     [1]      chr1   6600-6699 ---      chr1   6600-6699 |     FALSE  2.108420
#>     [2]      chr1   5698-5797 ---      chr1   5698-5797 |     FALSE  5.991699
#>     [3]      chr1 10386-10485 ---      chr1 10386-10485 |     FALSE  5.696525
#>     [4]      chr1   4119-4218 ---      chr1   4119-4218 |     FALSE  0.409923
#>     [5]      chr1   9577-9676 ---      chr1   9577-9676 |     FALSE  9.330107
#>     ...       ...         ... ...       ...         ... .       ...       ...
#>   [496]      chr1   1275-1374 ---      chr1   1275-1374 |     FALSE   3.27301
#>   [497]      chr1   4976-5075 ---      chr1   4976-5075 |     FALSE   8.05522
#>   [498]      chr1   3917-4016 ---      chr1   3917-4016 |     FALSE   2.01576
#>   [499]      chr1 10205-10304 ---      chr1 10205-10304 |     FALSE   6.60221
#>   [500]      chr1   1841-1940 ---      chr1   1841-1940 |     FALSE   7.79926
#>            feature3
#>         <character>
#>     [1]           c
#>     [2]           b
#>     [3]           b
#>     [4]           a
#>     [5]           b
#>     ...         ...
#>   [496]           b
#>   [497]           c
#>   [498]           a
#>   [499]           b
#>   [500]           c
#>   -------
#>   regions: 10500 ranges and 0 metadata columns
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths
unmatched(x)
#> GInteractions object with 9500 interactions and 3 metadata columns:
#>          seqnames1     ranges1     seqnames2     ranges2 |  feature1  feature2
#>              <Rle>   <IRanges>         <Rle>   <IRanges> | <logical> <numeric>
#>      [1]      chr1     501-600 ---      chr1     501-600 |     FALSE   3.28347
#>      [2]      chr1     502-601 ---      chr1     502-601 |     FALSE   7.12640
#>      [3]      chr1     503-602 ---      chr1     503-602 |     FALSE   1.92222
#>      [4]      chr1     504-603 ---      chr1     504-603 |     FALSE  10.24116
#>      [5]      chr1     505-604 ---      chr1     505-604 |     FALSE  10.17287
#>      ...       ...         ... ...       ...         ... .       ...       ...
#>   [9496]      chr1 10496-10595 ---      chr1 10496-10595 |     FALSE   1.23578
#>   [9497]      chr1 10497-10596 ---      chr1 10497-10596 |     FALSE   1.69671
#>   [9498]      chr1 10498-10597 ---      chr1 10498-10597 |     FALSE   6.11140
#>   [9499]      chr1 10499-10598 ---      chr1 10499-10598 |     FALSE   2.21657
#>   [9500]      chr1 10500-10599 ---      chr1 10500-10599 |     FALSE   5.33003
#>             feature3
#>          <character>
#>      [1]           e
#>      [2]           a
#>      [3]           b
#>      [4]           a
#>      [5]           c
#>      ...         ...
#>   [9496]           b
#>   [9497]           a
#>   [9498]           a
#>   [9499]           d
#>   [9500]           b
#>   -------
#>   regions: 10500 ranges and 0 metadata columns
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths