CellMix 1.6

Generating Marker Lists

Description

The functions documented here serve to generate marker lists and MarkerList-class objects. They are useful to develop and test deconvolution methods that use marker gene lists.

gmarkers is the work horse generator function. It can generate "fixed" or random plain list of marker, optionnally with names and/or values.

This is a shortcut for MarkerList(gmarkers(...))

It is a shorcut for gmarkers(..., shuffle=TRUE).

This is a shortcut for MarkerList(rmarkers(...))

Usage

gmarkers(n, k = -3, names = FALSE, values = FALSE, shuffle = FALSE)

gMarkerList(...)

rmarkers(...)

rMarkerList(...)

Arguments

n
number of marker sets to generate, e.g., the number of cell types in the data.
k
numeric (integer) value that specifies the number of markers per set. If a negative value is specified, then it is interpreted as a growing factor for successive sets of markers, e.g., the default k=-3 generates a first set of 3 markers (=3 x 1), a second set with 6 (= 2 x 3), a third with 9 (= 3 x 3), and so long.
names
specification for names. If a logical it indicates if names should be generated or not. If a single string, it indicates the prefix to use for the names, the default being “Marker.”. If a character vector, then it specifies the names of each marker, and must then contain at least as many unique elements as markers in the whole generated list.
values
specification for values. If a logical, it indicates if a value should be generated and associated to each marker. If a numeric vector, then it specifies the values to associate with each marker. The names of this vector are currently not used. If not shuffling (see argument shuffle) and values is a numeric vector, then it must contain at least as many unique elements as markers in the whole generated list.
shuffle
logical that indicate if the markers should be shuffled randomly. This is used only if fixed names or values have been specified.
...
arguments eventually passed to gmarkers.