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.
Examples
if (FALSE) {
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)
}