Functions producing a new vector (matrix) marker vector set from an existing matrix (vector) marker set.
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mrkVecToMat(object, vfcol = "markers", mfcol = "Markers") mrkMatToVec(object, mfcol = "Markers", vfcol = "markers") mrkMatAndVec(object, vfcol = "markers", mfcol = "Markers") showMrkMat(object, mfcol = "Markers") isMrkMat(object, fcol = "Markers") isMrkVec(object, fcol = "markers") mrkEncoding(object, fcol = "markers")
The name of the vector marker feature
variable. Default is
The name of the matrix marker feature
variable. Default is
A marker feature variable name.
Sub-cellular markers can be encoded in two different ways. Sets of
spatial markers can be represented as character vectors
factor, to be accurate), stored as
feature metadata, and proteins of unknown or uncertain
localisation (unlabelled, to be classified) are marked with the
"unknown" character. While very handy, this encoding
suffers from some drawbacks, in particular the difficulty to label
proteins that reside in multiple (possible or actual)
localisations. The markers vector feature data is typically named
markers. A new matrix encoding is also
supported. Each spatial compartment is defined in a column in a
binary markers matrix and the resident proteins are encoded with
1s. The markers matrix feature data is typically named
Markers. If proteins are assigned unique localisations only
(i.e. no multi-localisation) or their localisation is unknown
(unlabelled), then both encodings are equivalent. When the markers
are encoded as vectors, features of unknown localisation are
fData(object)[, fcol] == "unknown". For
matrix-encoded markers, unlabelled proteins are defined as
rowSums(fData(object)[, fcol]) == 0.
mrkVecToMat functions enable the
conversion from matrix (vector) to vector (matrix). The
mrkMatAndVec function generates the missing encoding from
the existing one. If the destination encoding already exists, or,
more accurately, if the feature variable of the destination
encoding exists, an error is thrown. During the conversion from
matrix to vector, if multiple possible label exists, they are
dropped, i.e. they are converted to
isMrkMat can be used to test if a
marker set is encoded as a vector or a matrix.
"matrix" depending on the
nature of the markers.
MSnSet with a new vector (matrix) marker
Laurent Gatto and Lisa Breckels
Other functions that operate on markers are
markerMSnSet. To add markers to an existing
MSnSet, see the
addMarkers function and
pRolocmarkers, for a list of suggested markers.
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