msdata by MsDataHub.readQFeautres vignette.readQFeaturesFromDIANN(multiplexing = 'dimethyl') example.replaceColnames() function (see Issue
258)readQFeaturesFromDIANN()
(see PR #249), contributed by Karolína Kryštofová.aggregateFeatures() (PR #255).aggregateFeatures() and readQFeatures()
(PR #255).longForm() methods (replacing longFormat(), now defunct).longForm,SummarizedExperiment, supporting rowvars and
colvars, as longForm,QFeatures does. Without this method, uses
longForm,ANY that doesn't.QFeatures object type (bulk or single-cell) in the
instance's metadata slot (developer features).keep = TRUE (see
issue 231).aggregateFeatures in the case of
multiple assays aggregation.nNA() on empty assays (see #174).fnames argument in readQFeatures(). The fnames argument is
not passed to readSummarizedExperiment() anymore, but used at in
readQFeatures(). Rownames are now set after splitting. Given that
rownames must be unique and that this was enforced with
make.unique(), the previous behaviour misnamed features that
should get the same name.readQFeatures() bug and adapted unit tests.QFeaturesQFeatures::longFormat() when rownames are numerical
(reported upstream https://github.com/waldronlab/MultiAssayExperiment/issues/331).reshape2::melt, required for
MultiAssayExperiment::longFormat().filterFeatures() when the filter variable also exists in the
global environment (issue #208)..splitS[C]E() unit test form scp to QFeatures.readQFeatres() params in readQFeatureFromDIANN().readQFeaturesFromDIANN().is.vector() (see issue #203)readQFeatures() multi-set support (ported from scp::readSCP() -
see issue #199).readQFeaturesFromDIANN() function to import DIA-NN report
files (ported from scp::readSCPfromDIANN() - see issue #199).filterFeatures generic method to ProtGenerics.nNA() and filterNA() and man pages to clarify percentages
and proportions (see #189).dropEmptyAssays() function (see issue #184).|> rather than %>%.selectRowData()c methods to combine QFeatures objects.nrows and ncols methods. Also added use.names argument
(cf ?BiocGenerics::dims)filterFeatures()filterFeatures()filterFeatures() to control whether
to keep or remove features for assays that do not contain the filter
variable. Also added message printing for a better overview of which
variable were found.addAssay() to solve issue #104.addAssay() and dramatically improved the usage
of computational resources.colData is automatically transferred from the assay to the
QFeatures object.removeAssay() and replaceAssay(). Together with
addAssay(), these functions are used to implement the replacement
method [[<- required to solve issue #57.adjacencyMatrix,SummarizedExperiment and
adjacencyMatrix,QFeatures methods using
ProtGenerics::adjacencyMatrix (available in version >= 1.27.1).updateObject() method for QFeatures objects.aggregateFeatures() and new adjacencyMatrix() accessor.feat3 example data to demonstrate and test more complex AssayLinks
structure.plot,QFeautres function to avoid cluttering of nodes.feat3.AssayLinksAssayLinks to ensure consistent datarbindRowData: a function to select variables in the rowData
and bind it in a single DataFramerowData<-: this new method replaces replaceRowDataCols to
offer a more standardize functionality.QFeatures vignette to expand on how to
manipulate the metadata within a QFeatures objectreplaceRowDataCols and removeRowDataCols, two functions
to streamline manipulation of rowData within a QFeature object.countUniqueFeatures, a function to count the number of
unique features per sample.Manually install preprocessCore (see https://github.com/Bioconductor/bioconductor_docker/issues/22 for details) to use quantile normalisation in vignette and tests.
Update vignette to show normalize() and logTransform() directly
on a QFeatures object and reference the QFeaturesWorkshop2020
workshop and WSBIM2122 chap 8.
nNA with new implementation and additional unit
tests <2020-10-23 Fri>longFormat function returns a long DataFrame
with quantitative data along with metadata (see #116)
<2020-10-8 Thu>rowData method returns a list containing the
rowData for all assays (see #86)
<2020-09-16 Wed>infIsNA.