test_differential_cellularity-methods: Add differential tissue composition information to a tbl

In tidybulk: Brings transcriptomics to the tidyverse

Description

test_differential_cellularity() takes as input a 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> | and returns a 'tbl' with additional columns for the statistics from the hypothesis test.

Usage

test_differential_cellularity(
  .data,
  .formula,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  method = "cibersort",
  reference = X_cibersort,
  significance_threshold = 0.05,
  ...
)

## S4 method for signature 'spec_tbl_df'
test_differential_cellularity(
  .data,
  .formula,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  method = "cibersort",
  reference = X_cibersort,
  significance_threshold = 0.05,
  ...
)

## S4 method for signature 'tbl_df'
test_differential_cellularity(
  .data,
  .formula,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  method = "cibersort",
  reference = X_cibersort,
  significance_threshold = 0.05,
  ...
)

## S4 method for signature 'tidybulk'
test_differential_cellularity(
  .data,
  .formula,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  method = "cibersort",
  reference = X_cibersort,
  significance_threshold = 0.05,
  ...
)

## S4 method for signature 'SummarizedExperiment'
test_differential_cellularity(
  .data,
  .formula,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  method = "cibersort",
  reference = X_cibersort,
  significance_threshold = 0.05,
  ...
)

## S4 method for signature 'RangedSummarizedExperiment'
test_differential_cellularity(
  .data,
  .formula,
  .sample = NULL,
  .transcript = NULL,
  .abundance = NULL,
  method = "cibersort",
  reference = X_cibersort,
  significance_threshold = 0.05,
  ...
)

Arguments

.data	A 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> |
.formula	A formula with no response variable, representing the desired linear model. If censored regression is desired (coxph) the formula should be of the form \"survival::Surv\(y, dead\) ~ x\"
.sample	The name of the sample column
.transcript	The name of the transcript/gene column
.abundance	The name of the transcript/gene abundance column
method	A string character. Either \"cibersort\" or \"llsr\"
reference	A data frame. The transcript/cell_type data frame of integer transcript abundance
significance_threshold	A real between 0 and 1 (usually 0.05).
...	Further parameters passed to the method deconvolve_cellularity

Details

\lifecycle

maturing

This routine applies a deconvolution method (e.g., Cibersort; DOI: 10.1038/nmeth.3337) and passes the proportions inferred into a generalised linear model (DOI:dx.doi.org/10.1007/s11749-010-0189-z) or a cox regression model (ISBN: 978-1-4757-3294-8)

Underlying method for the generalised linear model: data deconvolve_cellularity( !!.sample, !!.transcript, !!.abundance, method=method, reference = reference, action="get", ... ) [..] betareg::betareg(.my_formula, .)

Underlying method for the cox regression: data deconvolve_cellularity( !!.sample, !!.transcript, !!.abundance, method=method, reference = reference, action="get", ... ) [..] mutate(.proportion_0_corrected = .proportion_0_corrected survival::coxph(.my_formula, .)

Value

A 'tbl' with additional columns for the statistics from the hypothesis test (e.g., log fold change, p-value and false discovery rate).

A 'tbl' with additional columns for the statistics from the hypothesis test (e.g., log fold change, p-value and false discovery rate).

A 'tbl' with additional columns for the statistics from the hypothesis test (e.g., log fold change, p-value and false discovery rate).

A 'tbl' with additional columns for the statistics from the hypothesis test (e.g., log fold change, p-value and false discovery rate).

A 'SummarizedExperiment' object

A 'SummarizedExperiment' object

Examples

	test_differential_cellularity(
	 tidybulk::counts_mini,
	    ~ condition,
	    sample,
	    transcript,
	    count,
	    cores = 1
	)

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