LongTable-class {CoreGx} | R Documentation |
Define a private constructor method to be used to build a
LongTable
object.
This is used as an alternative to R attributes for storing structural metadata of an S4 objects.
Add or replace an assay in a LongTable by name. Currently this function only works when the assay has all columns in row and column data tables (i.e., when assays is retured withDimnames=TRUE). This will be fixed in future updates.
Select an assay from within a LongTable object.
## S4 method for signature 'LongTable' rowIDs(object, data = FALSE, key = FALSE) ## S4 method for signature 'LongTable' rowMeta(object, data = FALSE, key = FALSE) ## S4 method for signature 'LongTable' colIDs(object, data = FALSE, key = FALSE) ## S4 method for signature 'LongTable' colMeta(object, data = FALSE, key = FALSE) ## S4 method for signature 'LongTable' assayCols(object, i) ## S4 method for signature 'LongTable,character' getIntern(object, x, ...) ## S4 method for signature 'LongTable,missing' getIntern(object, x) ## S4 method for signature 'LongTable' rowData(x, key = FALSE, use.names = FALSE) ## S4 replacement method for signature 'LongTable' rowData(x) <- value ## S4 method for signature 'LongTable' colData(x, key = FALSE) ## S4 replacement method for signature 'LongTable,ANY' colData(x) <- value ## S4 method for signature 'LongTable' assays(x, withDimnames = TRUE, metadata = withDimnames, key = !withDimnames) ## S4 replacement method for signature 'LongTable,list' assays(x) <- value ## S4 method for signature 'LongTable,ANY' assay(x, i, withDimnames = FALSE, metadata = withDimnames, key = !withDimnames) ## S4 replacement method for signature 'LongTable,character' assay(x, i) <- value ## S4 method for signature 'LongTable' assayNames(x) ## S4 method for signature 'LongTable,ANY,ANY' x[[i, withDimnames = TRUE, metadata = withDimnames, keys = !withDimnames]] ## S4 method for signature 'data.frame' buildLongTable(from, rowDataCols, colDataCols, assayCols) ## S4 method for signature 'character' buildLongTable(from, rowDataCols, colDataCols, assayCols) ## S4 method for signature 'LongTable' dim(x) ## S4 method for signature 'LongTable' colnames(x) ## S4 method for signature 'LongTable' rownames(x) ## S4 method for signature 'LongTable' dimnames(x)
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LongTable
object containing the assay data from a treatment
response experiment
A character
vector of rowData column names if data is FALSE,
otherwise a data.table
with the data from the rowData id columns.
A character
vector of rowData column names if data is FALSE,
otherwise a data.table
with the data from the rowData metadta columns.
A character
vector of colData column names if data is FALSE,
otherwise a data.table
with the data from the colData id columns.
A character
vector of colData column names if data is FALSE,
otherwise a data.table
with the data from the colData metadta columns.
A list
of character
vectors containing the value column names for
each assay if i is missing, otherwise a character
vector of value column
names for the selected assay.
value of x if length(x) == 1 else named list of values for all symbols in x
A named list
with all values in environment object@.intern coerced
to a list (and therefore copied).
A data.table
containing rowID, row identifiers, and row metadata.
A copy of the LongTable
object with the rowData
slot updated.
A data.table
containing row identifiers and metadata.
A copy of the LongTable
object with the colData
slot updated.
A list
of data.table
objects, one per assay in the object.
A copy of the LongTable
with the assays modified.
LongTable
With updated assays slot.
character
Names of the assays contained in the LongTable
.
A LongTable
object containing one or more assays, indexed by
rowID and colID.
A LongTable
object containing one or more assays, indexed by
rowID and colID.
numeric
Vector of object dimensions.
character
Vector of column names.
character
Vector of row names.
list
List with two character vectors, one for row and one for
column names.
rowMeta
: Get the names of the non-id columns from rowData.
colIDs
: Get the names of the columns in colData required to
uniquely identify each row.
colMeta
: Get the names of the non-id columns in the colData
data.table
.
assayCols
: Get a list of column names for each assay in a
LongTable
.
getIntern
: Access structural metadata present within a
LongTable object. This is mostly for developmer use.
getIntern
: Access all structural metadata present within a
LongTable object. This is mostly for developmer use.
rowData
: Get the row level annotations for a LongTable
object.
rowData<-
: Update the row annotations for a LongTable
object.
Currently requires that all columns in rowIDs(longTable) be present in
value.
colData
: Get the column level annotations for a LongTable
object.
colData<-
: Upadte the colData of a LongTable object. Currently
requires that all of the colIDs(longTable) be in the value object.
assays
: Get a list containing all the assays in a LongTable
.
assays<-
: Update the assays in a LongTable object. The rowIDs
and colIDs must be present in all assays to allow successfully remapping
the keys. We recommend modifying the list returned by
assays(longTable, withDimnames=TRUE) and the reassigning to the
LongTable
.
assay
: Retrieve an assay data.table
object from the
assays
slot of a LongTable
object.
assay<-
:
assayNames
: Return the names of the assays contained in a
LongTable
[[
: Get an assay from a LongTable object. This method
returns the row and column annotations by default to make assignment
and aggregate operations easiers.
buildLongTable
: Create a LongTable object from a single data.table or
data.frame object.
buildLongTable
: Create a LongTable object from a single .csv file
dim
: Get the number of row annotations by the number of
column annotations from a LongTable object. Please note that row x columns
does not necessarily equal the number of rows in an assay, since it is
not required for each assay to have every row or column present.
colnames
: Retrieve the pseudo-colnames of a LongTable object,
these are constructed by pasting together the colIDs(longTable) and
can be used in the subset method for regex based queries.
rownames
: Retrieve the pseudo-rownames of a LongTable object,
these are constructed by pasting together the rowIDs(longTable) and
can be used in the subset method for regex based queries.
dimnames
: Get the pseudo-dimnames for a LongTable object. See
colnames and rownames for more information.
rowData
See Slots section.
colData
See Slots section.
assays
See Slots section.
metadata
See Slots section.
.intern
See Slots section.
rowData: A data.table
containing the metadata associated with the
row dimension of a LongTable
.
colData: A data.table
containing the metadata associated with the
column dimension of a LongTable
.
assays: A list
of data.table
s, one for each assay in a
LongTable
.
metadata: An optional list
of additional metadata for a LongTable
which doesn't map to one of the dimensions.
.intern: An environment
that holds internal structural metadata
about a LongTable object, such as which columns are required to key
the object. An environment has been used to allow locking items, which
can prevent accidental modification of a property required for the class
to work.
rowIDs(merckLongTable) rowMeta(merckLongTable) colIDs(merckLongTable) colMeta(merckLongTable) assayCols(merckLongTable) getIntern(merckLongTable, 'rowIDs') getIntern(merckLongTable, c('colIDs', 'colMeta')) getIntern(merckLongTable) rowData(merckLongTable) rowData(merckLongTable) <- rowData(merckLongTable) colData(merckLongTable) # Get the keys as well, mostly for internal use colData(merckLongTable, key=TRUE) colData(merckLongTable) <- colData(merckLongTable) assays(merckLongTable) assays(merckLongTable) <- assays(merckLongTable, withDimnames=TRUE) # Default annotations, just the key columns assay(merckLongTable, 'sensitivity') assay(merckLongTable, 1) # With identifiers joined assay(merckLongTable, 'sensitivity', withDimnames=TRUE) # With identifiers and metadata assay(merckLongTable, 'profiles', withDimnames=TRUE, metadata=TRUE) assay(merckLongTable, 'sensitivity') <- assay(merckLongTable, 'sensitivity', withDimnames=TRUE) assay(merckLongTable, 'sensitivity') <- merckLongTable$sensitivity assayNames(merckLongTable) merckLongTable[['sensitivity']] dim(merckLongTable) dim(merckLongTable) head(colnames(merckLongTable)) head(rownames(merckLongTable)) lapply(dimnames(merckLongTable), head)