mrkConsProfiles: Marker consensus profiles

In lgatto/pRoloc: A unifying bioinformatics framework for spatial proteomics

Marker consensus profiles

Description

A function to calculate average marker profiles.

Usage

mrkConsProfiles(object, fcol = "markers", method = mean)

Arguments

object	An instance of class MSnSet.
fcol	Feature meta-data label (fData column name) defining the groups to be differentiated using different colours. Default is markers.
method	A function to average marker profiles. Default is mean.

Value

A matrix of dimensions number of clusters (exluding unknowns) by number of fractions.

Author(s)

Laurent Gatto and Lisa M. Breckels

See Also

The mrkHClust function to produce a hierarchical cluster.

Examples

library("pRolocdata")
data(dunkley2006)
mrkConsProfiles(dunkley2006)
mrkConsProfiles(dunkley2006, method = median)
mm <- mrkConsProfiles(dunkley2006)
## Reorder fractions
o <- order(dunkley2006$fraction)
## Plot mean organelle profiles using the
## default pRoloc colour palette.
matplot(t(mm[, o]), type = "l",
        xlab = "Fractions", ylab = "Relative intensity",
        main = "Mean organelle profiles",
        col = getStockcol(), lwd = 2, lty = 1)
## Add a legend
addLegend(markerMSnSet(dunkley2006), where = "topleft")

lgatto/pRoloc documentation built on March 14, 2024, 7:10 a.m.