deconvolve_cellularity,spec_tbl_df-method {tidybulk}R Documentation

deconvolve_cellularity

Description

deconvolve_cellularity

Usage

## S4 method for signature 'spec_tbl_df'
deconvolve_cellularity(
  .data,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  reference = X_cibersort,
  method = "cibersort",
  action = "add",
  ...
)

Arguments

.data

A 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> |

.sample

The name of the sample column

.transcript

The name of the transcript/gene column

.abundance

The name of the transcript/gene abundance column

reference

A data frame. The transcript/cell_type data frame of integer transcript abundance

method

A character string. The method to be used. At the moment Cibersort (default) and llsr (linear least squares regression) are available.

action

A character string. Whether to join the new information to the input tbl (add), or just get the non-redundant tbl with the new information (get).

...

Further parameters passed to the function Cibersort

Value

A 'tbl' object including additional columns for each cell type estimated

[Package tidybulk version 0.99.23 Index]