seurat_to_combiroc: Load CombiROC data.

In combiroc: Selection and Ranking of Omics Biomarkers Combinations Made Easy

Load CombiROC data.

Description

A function to extract a combiroc data (both labelled and unlabelled) from a SeuratObject.

Usage

seurat_to_combiroc(
  SeuratObject,
  gene_list,
  assay = "RNA",
  labelled_data = F,
  case_class = NA,
  case_label = "case",
  control_label = "control"
)

Arguments

SeuratObject	Defines S4 classes for single-cell genomic data and associated information.
gene_list	a list of gene names.
assay	a character that specifies the assay of interest.
labelled_data	a boolean that specifies whether the combiroc data to be extracted must be labelled (with 'Class' column) or not.
case_class	a character or a character vector specifying the category/ies to be considered as 'case class'. Required if labelled_data is TRUE.
case_label	a character that will be assigned to the cells belonging to 'case class' category.
control_label	a character that will be assigned to the cells belonging to 'control class' category.

Details

By specifying a gene list (if the genes are in rownames of SeuratObject assay matrix, it subsets the gene expression matrix (@data) and it retreives their expression values. If a combiroc training dataset (labelled_data=T) is required, one or more categories of Idents(SeuratObject) must be selected as case_class, the others will be merged into control class.

Value

a combiroc data.

Examples

## Not run: 
demo_seurat# A subset of PBMC3K dataset from Satijia et al. 2015

# list of markers of interest
gene_list<-c('RBP7','CYP1B1','CD14','FCN1','NKG7', 'GNLY')

# to extract the combircoc data from data from pbmc3k.final (case class: Monocytes)
data <- seurat_to_combiroc(demo_seurat, gene_list = gene_list, labelled_data = TRUE,
                           case_class = c('CD14+ Mono','FCGR3A+ Mono'),
                           case_label = 'Monocyte', control_label='Other')
head(data)

## End(Not run)

combiroc documentation built on July 9, 2023, 5:56 p.m.