deconvolute: Devonvolute bulk RNA-seq data based on reference data

In quadbiolab/VoxHunt: Projecting single-cell transcriptomes to spatial brain maps

Devonvolute bulk RNA-seq data based on reference data

Description

Devonvolute bulk RNA-seq data based on reference data

Usage

## Default S3 method:
deconvolute(
  expr_mat,
  genes_use,
  reference = "ABA",
  stage = "E13",
  annotation_level = "custom_2",
  pseudo_tpm = FALSE,
  other_types = FALSE,
  involve_regions = NULL
)

deconvolute(object, ...)

Arguments

expr_mat	Expression matrix to deconvolute.
genes_use	Marker genes to use for deconvolution.
reference	Which reference to use.
stage	Developmental stage to use as reference.
other_types	Whether to infer proportions of type 'other'.

Value

A tibble with deconvoluted proportions for each reference structure.

quadbiolab/VoxHunt documentation built on March 4, 2024, 6:37 a.m.