R/AllGenerics.R, R/methods-utils.R
makeExampleMatchedDataSet.RdThis function will generate an example dataset as either 1) input
for matchRanges() (when matched = FALSE) or 2) a
Matched Object (when matched = TRUE).
makeExampleMatchedDataSet(
type = "DataFrame",
matched = FALSE,
method = "rejection",
replace = FALSE,
...
)
# S4 method for character_OR_missing,logical_OR_missing,character_OR_missing,logical_OR_missing
makeExampleMatchedDataSet(type, matched, method, replace)Character designating which type of dataset to make. options are one of 'data.frame', 'data.table', 'DataFrame', 'GRanges', or 'GInteractions'.
TRUE/FALSE designating whether to generate a
Matched dataset (matched = TRUE) or an input dataset
for matchRanges() (matched = FALSE).
Character describing which matching method to use. Supported options are either 'nearest', 'rejection', or 'stratified'.
TRUE/FALSE describing whether to select matches with or without replacement.
Additional arguments
Returns an example Matched dataset or an example dataset for
input to matchRanges().
When matched = FALSE, the data returned contains 3 different
features that can be subset to perform matching.
## Make examples for matchRanges() (i.e matched = FALSE)
set.seed(123)
makeExampleMatchedDataSet()
#> DataFrame with 10500 rows and 3 columns
#> feature1 feature2 feature3
#> <logical> <numeric> <character>
#> 1 TRUE 2.87905 c
#> 2 TRUE 3.53965 c
#> 3 TRUE 7.11742 c
#> 4 TRUE 4.14102 a
#> 5 TRUE 4.25858 c
#> ... ... ... ...
#> 10496 FALSE 1.23578 b
#> 10497 FALSE 1.69671 a
#> 10498 FALSE 6.11140 a
#> 10499 FALSE 2.21657 d
#> 10500 FALSE 5.33003 b
head(makeExampleMatchedDataSet(type = 'data.frame', matched = FALSE))
#> feature1 feature2 feature3
#> 1 TRUE 3.636514 c
#> 2 TRUE 1.330261 c
#> 3 TRUE 4.236877 c
#> 4 TRUE 4.042873 b
#> 5 TRUE 3.081029 b
#> 6 TRUE 6.058335 c
makeExampleMatchedDataSet(type = 'data.table', matched = FALSE)
#> feature1 feature2 feature3
#> 1: TRUE 0.2032325 c
#> 2: TRUE 7.4856837 d
#> 3: TRUE 1.8105119 b
#> 4: TRUE 4.3514990 c
#> 5: TRUE 8.1239122 b
#> ---
#> 10496: FALSE 2.2574409 a
#> 10497: FALSE 7.0427986 b
#> 10498: FALSE 9.5341569 d
#> 10499: FALSE 5.0367807 a
#> 10500: FALSE 1.7628214 b
makeExampleMatchedDataSet(type = 'DataFrame', matched = FALSE)
#> DataFrame with 10500 rows and 3 columns
#> feature1 feature2 feature3
#> <logical> <numeric> <character>
#> 1 TRUE 2.17220 c
#> 2 TRUE 4.15337 e
#> 3 TRUE 4.12367 c
#> 4 TRUE 3.43931 a
#> 5 TRUE 7.77699 a
#> ... ... ... ...
#> 10496 FALSE 1.046444 a
#> 10497 FALSE 8.549075 a
#> 10498 FALSE 0.454913 b
#> 10499 FALSE 0.358426 e
#> 10500 FALSE 4.262284 d
makeExampleMatchedDataSet(type = 'GRanges', matched = FALSE)
#> GRanges object with 10500 ranges and 3 metadata columns:
#> seqnames ranges strand | feature1 feature2 feature3
#> <Rle> <IRanges> <Rle> | <logical> <numeric> <character>
#> [1] chr1 1-100 * | TRUE 1.78381 c
#> [2] chr1 2-101 * | TRUE 6.14991 c
#> [3] chr1 3-102 * | TRUE 4.44694 d
#> [4] chr1 4-103 * | TRUE 2.97590 c
#> [5] chr1 5-104 * | TRUE 7.72256 b
#> ... ... ... ... . ... ... ...
#> [10496] chr1 10496-10595 * | FALSE 6.25657 a
#> [10497] chr1 10497-10596 * | FALSE 8.40767 b
#> [10498] chr1 10498-10597 * | FALSE 5.10310 b
#> [10499] chr1 10499-10598 * | FALSE 2.21031 b
#> [10500] chr1 10500-10599 * | FALSE 9.02046 c
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
makeExampleMatchedDataSet(type = 'GInteractions', matched = FALSE)
#> GInteractions object with 10500 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 3.68136
#> [2] chr1 2-101 --- chr1 2-101 | TRUE 6.20206
#> [3] chr1 3-102 --- chr1 3-102 | TRUE 3.18163
#> [4] chr1 4-103 --- chr1 4-103 | TRUE 3.12921
#> [5] chr1 5-104 --- chr1 5-104 | TRUE 5.95224
#> ... ... ... ... ... ... . ... ...
#> [10496] chr1 10496-10595 --- chr1 10496-10595 | FALSE 5.58682
#> [10497] chr1 10497-10596 --- chr1 10497-10596 | FALSE 6.65464
#> [10498] chr1 10498-10597 --- chr1 10498-10597 | FALSE 4.18161
#> [10499] chr1 10499-10598 --- chr1 10499-10598 | FALSE 4.87692
#> [10500] chr1 10500-10599 --- chr1 10500-10599 | FALSE 7.84910
#> feature3
#> <character>
#> [1] b
#> [2] a
#> [3] c
#> [4] c
#> [5] c
#> ... ...
#> [10496] a
#> [10497] b
#> [10498] d
#> [10499] d
#> [10500] a
#> -------
#> regions: 10500 ranges and 0 metadata columns
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
## Make Matched class examples (i.e. matched = TRUE)
set.seed(123)
makeExampleMatchedDataSet(matched = TRUE)
#> MatchedDataFrame with 500 rows and 3 columns
#> feature1 feature2 feature3
#> <logical> <numeric> <character>
#> 1 FALSE 2.108420 c
#> 2 FALSE 5.991699 b
#> 3 FALSE 5.696525 b
#> 4 FALSE 0.409923 a
#> 5 FALSE 9.330107 b
#> ... ... ... ...
#> 496 FALSE 3.27301 b
#> 497 FALSE 8.05522 c
#> 498 FALSE 2.01576 a
#> 499 FALSE 6.60221 b
#> 500 FALSE 7.79926 c
makeExampleMatchedDataSet(type = 'DataFrame', matched = TRUE,
method = 'rejection',
replace = FALSE)
#> MatchedDataFrame with 500 rows and 3 columns
#> feature1 feature2 feature3
#> <logical> <numeric> <character>
#> 1 FALSE 3.25187 c
#> 2 FALSE 8.18426 b
#> 3 FALSE 6.00364 c
#> 4 FALSE 5.56505 b
#> 5 FALSE 5.02590 b
#> ... ... ... ...
#> 496 FALSE 1.887820 c
#> 497 FALSE 0.259549 d
#> 498 FALSE 2.567883 d
#> 499 FALSE 4.346857 b
#> 500 FALSE 0.056791 c
makeExampleMatchedDataSet(type = 'GRanges', matched = TRUE,
method = 'rejection',
replace = FALSE)
#> MatchedGRanges object with 500 ranges and 3 metadata columns:
#> seqnames ranges strand | feature1 feature2 feature3
#> <Rle> <IRanges> <Rle> | <logical> <numeric> <character>
#> [1] chr1 8001-8100 * | FALSE 10.89607 d
#> [2] chr1 1710-1809 * | FALSE 5.75671 c
#> [3] chr1 8659-8758 * | FALSE 4.46443 c
#> [4] chr1 5458-5557 * | FALSE 4.11386 a
#> [5] chr1 8661-8760 * | FALSE 1.79914 b
#> ... ... ... ... . ... ... ...
#> [496] chr1 6728-6827 * | FALSE 6.20597 b
#> [497] chr1 1508-1607 * | FALSE 7.09604 c
#> [498] chr1 7528-7627 * | FALSE 2.43404 c
#> [499] chr1 3883-3982 * | FALSE 5.03960 c
#> [500] chr1 1378-1477 * | FALSE 3.08657 d
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
# throwing error (April 2023)
#makeExampleMatchedDataSet(type = 'GInteractions', matched = TRUE,
# method = 'rejection',
# replace = FALSE)