deconvolve_cellularity-methods: Get cell type proportions from samples

In tidybulk: Brings transcriptomics to the tidyverse

Description

deconvolve_cellularity() takes as input a 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> | and returns a 'tbl' with the estimated cell type abundance for each sample

Usage

deconvolve_cellularity(
  .data,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  reference = X_cibersort,
  method = "cibersort",
  action = "add",
  ...
)

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

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

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

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

## S4 method for signature 'RangedSummarizedExperiment'
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

Details

\lifecycle

maturing

This function infers the cell type composition of our samples (with the algorithm Cibersort; Newman et al., 10.1038/nmeth.3337).

Underlying method: CIBERSORT(Y = data, X = reference, ...)

Value

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

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

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

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

A 'SummarizedExperiment' object

A 'SummarizedExperiment' object

Examples

# Subsetting for time efficiency
deconvolve_cellularity(filter(tidybulk::counts, sample=="SRR1740034"), sample, transcript, `count`, cores = 1)

tidybulk documentation built on April 7, 2021, 6 p.m.