rnb.execute.ct.estimation: rnb.execute.ct.estimation
Description
Perform the estimation of the cell type contributions in each analyzed sample.
Usage
rnb.execute.ct.estimation(rnb.set, cell.type.column = NA, test.max.markers = NA, top.markers = 500, method = "houseman1", verbose = TRUE)
Arguments
rnb.set
object of class RnBSet
cell.type.column
integer index or character identifier of a column in sample annotation table of rnb.set
which gives the mapping of samples to reference cell types
test.max.markers
maximal amount of CpG positions to use for marker selection
top.markers
the number of markers to select
method
algorithm used for estmation of the cell type contributions
verbose
flag specifying whether diagnostic output should be written to the console
or to the RnBeads logger in case the latter is initialized
Value
object of class CellTypeInferenceResult
Details
The only supported method is the one from Houseman et al BMC Bioinformatics 2012