rnb.execute.ct.estimation {RnBeads} | R Documentation |
Perform the estimation of the cell type contributions in each analyzed sample.
rnb.execute.ct.estimation(rnb.set, cell.type.column = NA, test.max.markers = NA, top.markers = 500, method = "houseman1", verbose = TRUE)
rnb.set |
object of class |
cell.type.column |
integer index or character identifier of a column in sample annotation table of |
test.max.markers |
Maximal amount of CpG positions to use for marker selection. If this option is set to
|
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 |
The only supported method is the one from Houseman et al BMC Bioinformatics 2012
object of class CellTypeInferenceResult
Pavlo Lutsik