| subset,LongTable-method | R Documentation |
Subset method for a LongTable object.
Description
Allows use of the colData and rowData data.table objects to query based on
rowID and colID, which is then used to subset all assay data.tables stored
in the assays slot.
This function is endomorphic, it always returns a LongTable object.
Usage
## S4 method for signature 'LongTable'
subset(x, i, j, assays = assayNames(x), reindex = TRUE)
Arguments
x |
LongTable The object to subset.
|
i |
character, numeric, logical or call
Character: pass in a character vector of rownames for the LongTable object
or a valid regex query which will be evaluated against the rownames.
Numeric or Logical: vector of indices or a logical vector to subset
the rows of a LongTable.
Call: Accepts valid query statements to the data.table i parameter,
this can be used to make complex queries using the data.table API
for the rowData data.table.
|
j |
character, numeric, logical or call
Character: pass in a character vector of colnames for the LongTable object
or a valid regex query which will be evaluated against the colnames.
Numeric or Logical: vector of indices or a logical vector to subset
the columns of a LongTable.
Call: Accepts valid query statements to the data.table i parameter,
this can be used to make complex queries using the data.table API
for the colData data.table.
|
assays |
character, numeric or logical Optional list of assay
names to subset. Can be used to subset the assays list further,
returning only the selected items in the new LongTable.
|
reindex |
logical(1) Should index values be reset such that they
are the smallest possible set of consecutive integers. Modifies the
"rowKey", "colKey", and all assayKey columns. Initial benchmarks indicate
reindex=FALSE saves ~20% of both execution time and memory allocation. The
cost of reindexing decreases the smaller your subset gets.
|
Value
LongTable A new LongTable object subset based on the specified
parameters.
Examples
# Character
subset(merckLongTable, 'ABT-888', 'CAOV3')
# Numeric
subset(merckLongTable, 1, c(1, 2))
# Logical
subset(merckLongTable, , colData(merckLongTable)$sampleid == 'A2058')
# Call
subset(merckLongTable, drug1id == 'Dasatinib' & drug2id != '5-FU',
sampleid == 'A2058')
