NEWS.md
[[<-
, the re-ordering of assays based on the value input was invalid when empty assays present (@danielinteractive, #322).assays
also updates the order of names in the MultiAssayExperiment
and assays in the sampleMap
replicates
provides the actual colname
s identified as replicate observations for a particular biological unit in the sampleMap
assay<-
replacement method for robustifying saveHDF5MultiAssayExperiment
with plain matricesBiocBaseUtils::setSlots
and avoid warnings of triple colon use.colData
has one column when merging two MultiAssayExperiment
objects, i.e., using the c
method (@cvanderaa, #315)colnames
and rownames
methods (@cvanderaa, #314)saveHDF5MultiAssayExperiment
and loadHDF5MultiAssayExperiment
(@asiyeka, #313)replicated
methodwideFormat
documentation, when replicates present additional sets of columns will be appended to the produced DataFrame
(@DarioS, #312)subsetByColData
and remove harmonization (@cvanderaa, #302)getWithColData
suppresses messages from natural subsetting operations by default with verbose = FALSE
(@bhagwataditya, #301)getWithColData
was using the old default (drop = TRUE
) and causing an error when the experiment is empty (@danielinteractive, #300)..harmonize
operation are reduced to increase memory efficiency, when identical experiment colnames present (@LTLA, #299).subsetByColData
now errors on subscript vectors longer than the nrow
of the colData
(previously a warning
).colData<-
includes a check for identical row names. If so, direct replacement of the colData
occurs without harmonization.sampleMap
is provided in the constructor function which may cause unexpected behavior. Documentation is updated to include more details on the sampleMap
input.saveHDF5MultiAssayExperiment
allows users to save data from most classes (excluding RaggedExperiment
) into a single H5 file (ctb @hpages)MultiAssayExperimentToMAF
(ctb @PoisonAlien)renameColname
and renamePrimary
provide renaming facilities for column names in experiments and rownames
in the colData
, respectivelycolnames(mae) <- value
colData
or experiments
(including [[<-
), new rownames
and colnames
(respectively) are checked against existing values and an error is given when none matchList
objects to replace the data in the ExperimentList
is now supportedsplitAssay
allows users to separate / split columns across assaysmakeHitList
is a facilitator function to create the logical lists that are required as input to splitAssay
drop
argument when subsetting a MultiAssayExperiment
is now FALSE
by defaultmergeReplicates
longFormat
with character assay matrices (@jonocarroll, #282)colData
rownames and ExperimentList
colnames are empty (@LTLA #262)ExperimentList
(@lgatto, #265)ExperimentList
element columns (@lwaldron)MultiAssayExperiment
and MatchedAssayExperiment
(@lgatto, #267 #268, @lwaldron)j
in mae[i, j, k]
is longer than colData
rowsclass(matrix())
UpsetSamples
more robust to differences in names between split sampleMap
and names(ExperimentList)
(@jonocarroll, #269)UpsetSamples
ExperimentList
propagation of mcols
and metadata
(@vobencha, #270)validObject
with replacement methods colData
and sampleMap
(@vobencha, #271)MultiAssayExperiment
class schematic now included (@mtmorgan, #261)upsetSamples
functionsplitAsList
from S4Vectors
(@hpages)ExperimentList
when replacing it inside a MultiAssayExperiment
object (@lawremi, #259)getWithColData
now allows easy extraction of experiments (such as SummarizedExperiment
) with associated colData
dataMultiAssayExperiment
assaysisEmpty
method fixed for ExperimentList
s containing matricesMultiAssayExperiment
now inherits from the standard Annotated
virtual classc
method better distinguishes between list
and ExperimentList
inputs.getHits
internal method for obtaining correct queries on row metadataNULL
rows compared to empty rows (i.e., character(0L)
)[<-
added to support assignment of assay datasetsnames(x) <- value
replicated
and mergeReplicates
functions have been refactored and improvedc
functionMultiAssayExperiment
by a list
or List
type class now returns experiments in the input order for rows, columns, and assayswideFormat
function improvements and bug fixes with name indicator subsettingBiocGenerics:::replaceSlots
used instead of replace methodsanyReplicated
, c
, and names<-
functionsimportFrom
directivescolnames
listToMap
re-written for efficiencysubsetByAssay
bug fixed when using an integer index (@vjcitn, #)DataFrame
now exported for users (@DarioS, #242)c
is smarter at matching colnames
with primary
names and creating a sampleMap
MatchedAssayExperiment
constructor function now works either a single MultiAssayExperiment
or the essential components of one.duplicated
function to replicated
List
and list
to ExperimentList
wideFormat
)clusterOn
function and move to Bioconductor/MultiOmicQC
package on GitHubreplicated
and anyReplicated
tidyr
and reshape2
try()
pData
RangedRaggedAssay
list
/List
class subsettorsisEmpty
method for ExperimentList
to account for an empty matrixMultiAssayExperiment-class
and MultiAssayExperiment-helpers
c
internals improvedDataFrame
in ExperimentList
[
)wideFormat
column namesupsetSamples
does not munge experiment names with special characters when check.names = FALSE
(by default keeps hyphens, underscores, etc.). A nameFilter
functional argument allows operations such as substr
on the experiment names. (@vjcitn, #231)prepMultiAssay
duplicated
function now returns FALSE for non-duplicated samplesExperimentList
constructor now handles multiple key = value
entriesupdateObject
before giving warningRTCGAToolbox
example vignetteExpressionSet
legacy objects)rearrange
is now broken up into longFormat
and wideFormat
functions.?'MultiAssayExperiment-helpers'
MultiAssayExperiment
quickstart guide vignette addedRangedRaggedAssay
class. Use RaggedExperiment
package instead.reduce
function simplifiedmapFrom
convenience argument added to the c,MultiAssayExperiment-method
assay
and assays
methods have been revised to conform to SummarizedExperiment
standardsAPI()
now points to the correct web documentExperimentList
constructor no longer coerces GRangesList
to RangedRaggedAssay
experiments
, experiments<-
, sampleMap
, and sampleMap<-
getHits
method, simplified helper function in placeprepMultiAssay
helper now returns a list
with names corresponding to the MultiAssayExperiment
constructor functionMatchedAssayExperiment
subclass added for matched samples in all assaysdata(miniACC)
drop = FALSE
in single column subset of colDatac
vignette section for adding experiments to an existingc
method implemented for experiments with 1:1 sample matches in pData
rowsMultiAssayExperiment
show method improved[[
extracts single experiment (replacement also included)getHits
methods removed and refactored subsetByRows
subsetBypData
availablerearrange
method now supports “wide” format outputsextract
method now available for common classes - creates tidy
data.frame from datadimnames
method added to RangedRaggedAssay
$
(DollarSign) method available for MultiAssayExperiment
to access pData
columnmetadata<-
set method now available for the MultiAssayExperiment
MultiAssayExperiment
constructor with renamed argument “experiments” for the ExperimentList
or list
input.updateObject
method now available for old instances of the MultiAssayExperiment
MultiAssayExperiments
should update and re-serialize themcomplete.cases
method available for the MultiAssayExperiment
classsampleMap
column names renamed to assay (prev. “assayname”), primary, and colname (prev. “assay”)MultiAssayExperiment
objects with TCGA dataElist
class renamed to ExperimentList
ExperimentList
constructor is homonymousExperimentList
accessor now called experiments
ExperimentList
replacement method is now experiments<-
assay
method for RangedRaggedAssay
works on inner metadata columns nowHDF5Array
packageassay
method available for RangedRaggedAssay
and other classes. Created to obtain raw data from certain classes (see ?assay,(class),ANY-method
).PrepMultiAssay
helper function now available to aid in creating object (#122)colnames
now available for the RangedRaggedAssay
class.RangedRaggedAssay
rowname constructionshow
method for the RangedRaggedAssay
classMultiAssayExperiment
constructor now handles stray assays, colnames, pData rownames, and sampleMap
rowsmetadata
argument available in the MultiAssayExperiment
constructor functiondrop
argument now works as intended when using List
inherited objectsdimnames
method added to MultiAssayExperiment
MultiAssayExperiment
constructorshow
method displayExperimentList
argument providedsubset
function removedsampleMap
uses character vectors instead of Rle
Elist
order consistent when subsettingmapToList
preserves list order