rnb.execute.ct.estimation

Description

Perform the estimation of the cell type contributions in each analyzed sample.

Usage

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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. If this option is set to NA or NULL, all sites are considered. Please take into account the extended computation time in such a case.

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

Details

The only supported method is the one from Houseman et al BMC Bioinformatics 2012

Value

object of class CellTypeInferenceResult

Author(s)

Pavlo Lutsik

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