deconvolve_cellularity {tidybulk}R Documentation

Get cell type proportions from samples

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 = NULL,
  method = "cibersort",
  prefix = "",
  action = "add",
  ...
)

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

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

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

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

## S4 method for signature 'RangedSummarizedExperiment'
deconvolve_cellularity(
  .data,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  reference = NULL,
  method = "cibersort",
  prefix = "",
  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. If NULL, the default reference will be used for each algorithm. For llsr will be LM22.

method

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

prefix

A character string. The prefix you would like to add to the result columns. It is useful if you want to reshape data.

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

'r lifecycle::badge("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


library(dplyr)

# Subsetting for time efficiency
tidybulk::se_mini %>% tidybulk() %>% filter(sample=="SRR1740034") %>% deconvolve_cellularity(sample, feature, count, cores = 1)



[Package tidybulk version 1.4.0 Index]