rnb.execute.ct.estimation {RnBeads} | R Documentation

## 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. 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

[Package RnBeads version 2.12.2 Index]