addMarkers: Adds markers to the data

Description

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.

Usage

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

Arguments

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.

Value

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

Details

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.

Examples

Run this code

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)