addMarkers: Adds markers to the data
In pRoloc: A unifying bioinformatics framework for spatial proteomics

Description Usage Arguments Details Value Author(s) See Also Examples

The function adds a 'markers' feature variable. These markers are read from a comma separated values (csv) spreadsheet file. This markers file is expected to have 2 columns (others are ignored) where the first is the name of the marker features and the second the group label. Alternatively, a markers named vector as provided by the pRolocmarkers function can also be used.

1	addMarkers(object, markers, mcol = "markers", fcol, verbose = TRUE)

`object`	An instance of class `MSnSet`.
`markers`	A `character` with the name the markers' csv file or a named character of markers as provided by `pRolocmarkers`.
`mcol`	A `character` of length 1 defining the feature variable label for the newly added markers. Default is `"markers"`.
`fcol`	An optional feature variable to be used to match against the markers. If missing, the feature names are used.
`verbose`	A `logical` indicating if number of markers and marker table should be printed to the console.

It is essential to assure that featureNames(object) (or fcol, see below) and marker names (first column) match, i.e. the same feature identifiers and case fold are used.

A new instance of class MSnSet with an additional markers feature variable.

Laurent Gatto

See pRolocmarkers for a list of spatial markers and markers for details about markers encoding.

library("pRolocdata")
data(dunkley2006)
atha <- pRolocmarkers("atha")
try(addMarkers(dunkley2006, atha)) ## markers already exists
fData(dunkley2006)$markers.org <- fData(dunkley2006)$markers
fData(dunkley2006)$markers <- NULL
marked <- addMarkers(dunkley2006, atha)
fvarLabels(marked)
## if 'makers' already exists
marked <- addMarkers(marked, atha, mcol = "markers2")
fvarLabels(marked)
stopifnot(all.equal(fData(marked)$markers, fData(marked)$markers2))
plot2D(marked)
addLegend(marked, where = "topleft", cex = .7)