MatchedGInteractions: MatchedGInteractions objects

In nullranges/nullranges: Generation of null ranges via bootstrapping or covariate matching

MatchedGInteractions objects

Description

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.

See Also

InteractionSet::GInteractions

matchedData, covariates, method, withReplacement, indices

focal, pool, matched, unmatched

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)

## Make MatchedGInteractions example
set.seed(123)
x <- makeExampleMatchedDataSet(type = "GInteractions", matched = TRUE)
## Accessor functions for Matched class
matchedData(x)
covariates(x)
method(x)
withReplacement(x)
head(indices(x, set = 'matched'))

## Accessor functions for Matched subclasses
focal(x)
pool(x)
matched(x)
unmatched(x)

nullranges/nullranges documentation built on Aug. 29, 2023, 12:13 a.m.