R: Compute the number of non-zero values in each marker classes

zerosInBinMSnSet {pRoloc}

R Documentation

Compute the number of non-zero values in each marker classes

Description

The function assumes that its input is a binary MSnSet and computes, for each marker class, the number of non-zero expression profiles. The function is meant to be used to produce heatmaps (see the example) and visualise binary (such as GO) MSnSet objects and assess their utility: all zero features/classes will not be informative at all (and can be filtered out with filterBinMSnSet) while features/classes with many annotations (GO terms) are likely not be be informative either.

Usage

zerosInBinMSnSet(object, fcol = "markers", as.matrix = TRUE,
  percent = TRUE)

Arguments

`object`	An instance of class `MSnSet` with binary data.
`fcol`	A `character` defining the feature data variable to be used as markers. Default is `"markers"`.
`as.matrix`	If `TRUE` (default) the data is formatted and returned as a `matrix`. Otherwise, a `list` is returned.
`percent`	If `TRUE`, percentages are returned. Otherwise, absolute values.

Value

A matrix or a list indicating the number of non-zero value per marker class.

Author(s)

Laurent Gatto

Examples

library(pRolocdata)
data(hyperLOPIT2015goCC)
zerosInBinMSnSet(hyperLOPIT2015goCC)
zerosInBinMSnSet(hyperLOPIT2015goCC, percent = FALSE)
pal <- colorRampPalette(c("white", "blue"))
library(lattice)
levelplot(zerosInBinMSnSet(hyperLOPIT2015goCC),
          xlab = "Number of non-0s",
          ylab = "Marker class",
          col.regions = pal(140))

[Package pRoloc version 1.27.6 Index]