MultiAssayExperiment-helpers {MultiAssayExperiment} | R Documentation |
A set of helper functions were created to help clean and
manipulate a MultiAssayExperiment object. intersectRows
also works
for ExperimentList
objects.
complete.cases: Returns a logical vector corresponding to 'colData' rows that have data across all experiments
isEmpty: Returns a logical TRUE
value for zero length
MultiAssayExperiment
objects
intersectRows: Takes all common rows across experiments, excludes experiments with empty rownames
intersectColumns: A wrapper for complete.cases
to return a
MultiAssayExperiment
with only those biological units that have
measurements across all experiments
replicated: A function that identifies multiple samples that originate from a single biological unit within each assay
anyReplicated: Displays which assays have replicate measurements
mergeReplicates: A function that combines replicated / repeated measurements across all experiments and is guided by the replicated return value
longFormat: A MultiAssayExperiment
method that
returns a small and skinny DataFrame. The colDataCols
arguments allows the user to append colData
columns to the data.
wideFormat: A function to return a wide DataFrame where
each row represents an observation. Optional colDataCols
can be
added when using a MultiAssayExperiment
.
hasRowRanges: A function that identifies ExperimentList elements that have a rowRanges method
getWithColData: A convenience function for extracting an assay and associated colData
## S4 method for signature 'MultiAssayExperiment' complete.cases(...) ## S4 method for signature 'MultiAssayExperiment' isEmpty(x) intersectRows(x) intersectColumns(x) replicated(x) ## S4 method for signature 'MultiAssayExperiment' replicated(x) anyReplicated(x) ## S4 method for signature 'MultiAssayExperiment' anyReplicated(x) mergeReplicates(x, replicates = list(), simplify = BiocGenerics::mean, ...) ## S4 method for signature 'MultiAssayExperiment' mergeReplicates(x, replicates = replicated(x), simplify = BiocGenerics::mean, ...) ## S4 method for signature 'ANY' mergeReplicates(x, replicates = list(), simplify = BiocGenerics::mean, ...) longFormat(object, colDataCols = NULL, i = 1L) wideFormat(object, colDataCols = NULL, check.names = TRUE, collapse = "_", i = 1L) hasRowRanges(x) ## S4 method for signature 'MultiAssayExperiment' hasRowRanges(x) ## S4 method for signature 'ExperimentList' hasRowRanges(x) getWithColData(x, i)
... |
Additional arguments. See details for more information. |
x |
A MultiAssayExperiment or ExperimentList |
replicates |
A list of LogicalLists
indicating multiple / duplicate entries for each biological unit per assay,
see |
simplify |
A function for merging repeat measurements in experiments
as indicated by the |
object |
Any supported class object |
colDataCols |
A |
i |
The assay indicator for SummarizedExperiment objects (default 1L) |
check.names |
(logical default TRUE) Column names of the output
|
collapse |
(character default "_") A single string delimiter for output
column names. In |
The replicated
function finds replicate measurements in each
assay and returns a list of LogicalLists.
Each element in a single LogicalList corresponds to a
biological or primary unit as in the sampleMap
. Below is a
small graphic for one particular biological unit in one assay, where the
logical vector corresponds to the number of measurements/samples in the
assay:
> replicated(MultiAssayExperiment) (list str) '-- $ AssayName (LogicalList str) '-- [[ "Biological Unit" ]] Replicated if sum(...) > 1 '-- TRUE TRUE FALSE FALSE
anyReplicated
determines if any of the assays have at least one
replicate. Note. These methods are not available for the
ExperimentList
class due to a missing sampleMap
structure
(by design).
The mergeReplicates
function is a house-keeping method
for a MultiAssayExperiment
where only complete.cases
are
returned, replicate measurements are averaged (by default), and columns are
aligned by the row order in colData
. Additional arguments can be
passed on to the simplify
function.
The mergeReplicates
"ANY" method consolidates duplicate
measurements for rectangular data structures, returns object of the same
class (endomorphic). The ellipsis or ...
argument allows the
user to provide additional arguments to the simplify
functional
argument.
The longFormat
"ANY" class method, works with classes such as
ExpressionSet and SummarizedExperiment as well as matrix
to provide a consistent long and skinny DataFrame.
The hasRowRanges
method identifies assays that support
a rowRanges method and
return a GRanges object.
The mergeReplicates
function makes use of the output from
replicated
which will point out the duplicate measurements by
biological unit in the MultiAssayExperiment
. This function will return
a MultiAssayExperiment
with merged replicates. Additional arguments
can be provided to the simplify argument via the ellipsis (...).
The longFormat method takes data from the ExperimentList
in a MultiAssayExperiment
and returns a uniform
DataFrame
. The resulting DataFrame has columns indicating
primary, rowname, colname and value. This method can optionally include
colData columns with the colDataCols
argument
(MultiAssayExperiment
method only). The i
argument
allows the user to specify the assay value in a
SummarizedExperiment. It directly relates to the i
argument in the assay method.
The wideFormat
function returns standardized wide DataFrame
where each row represents a biological unit as in the colData
.
Depending on the data and setup, biological units can be patients, tumors,
specimens, etc. Optionally, colData
columns can be added to the
wide data output (see the colDataCols
argument). Metadata columns are
generated based on the names produced in the wide format
DataFrame. These can be accessed via the
mcols function. See the Arguments
and
longFormat
sections for argument descriptions.
The hasRowRanges
method identifies assays with associated ranged
row data by directly testing the method on the object. The result from the
test must be a GRanges class object to satisfy the test.
The getWithColData
function allows the user to conveniently extract
a particular assay as indicated by the i
index argument. It
will also attempt to provide the
colData
along with the
extracted object using the colData<-
replacement
method when possible. Typically, this method is available for
SummarizedExperiment and RaggedExperiment
classes.