MatchedDataFrame: MatchedDataFrame objects

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

MatchedDataFrame objects

Description

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

Details

The MatchedDataFrame class uses a delegate object during initialization to assign its DFrame slots. MatchedDataFrame behaves as a DataFrame but also includes additional Matched object functionality (see ?Matched). For more information about DataFrame see ?S4Vectors::DataFrame.

Slots

focal

A DataFrame object containing the focal data to match.

pool

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

delegate

A DataFrame object used to initialize DataFrame-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.

rownames

rownames(delegate)

nrows

nrows(delegate)

listData

as.list(delegate)

elementType

elementType(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

S4Vectors::DataFrame

matchedData, covariates, method, withReplacement, indices

focal, pool, matched, unmatched

Examples

## Constructing MatchedDataFrame with matchRanges
## data.frame
set.seed(123)
x <- makeExampleMatchedDataSet(type = "data.frame")
mx <- matchRanges(
  focal = x[x$feature1, ],
  pool = x[!x$feature1, ],
  covar = ~ feature2 + feature3,
  method = "rejection",
  replace = FALSE
)
class(mx)

## data.table
set.seed(123)
x <- makeExampleMatchedDataSet(type = "data.table")
mx <- matchRanges(
  focal = x[x$feature1],
  pool = x[!x$feature1],
  covar = ~ feature2 + feature3,
  method = "rejection",
  replace = FALSE
)
class(mx)

## DataFrame
set.seed(123)
x <- makeExampleMatchedDataSet(type = "DataFrame")
mx <- matchRanges(
  focal = x[x$feature1, ],
  pool = x[!x$feature1, ],
  covar = ~ feature2 + feature3,
  method = "rejection",
  replace = FALSE
)
class(mx)

## Make MatchedDataFrame example
set.seed(123)
x <- makeExampleMatchedDataSet(type = "DataFrame", 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.