createPALMOfromsinglecellmatrix: createPALMOfromsinglecellmatrix Function

In aifimmunology/PALMO: Identify Intra and Inter-Donor Variations in Bulk or Single Cell Longitudinal Dataset

createPALMOfromsinglecellmatrix Function

Description

This function allows to create Seurat object from counts and metadata as mentioned in https://search.r-project.org/CRAN/refmans/SeuratObject/html/CreateSeuratObject.html. The seurat object then stored in a newly created PALMO object.

Usage

createPALMOfromsinglecellmatrix(data, metadata, anndata = NULL)

Arguments

data	Expression matrix or data frame. Rows represents gene/proteins column represents participant samples (same as annotation table Sample column)
metadata	Metadata associated with singe cell information. For example rownames are unique cell_barcode and columns are information on each cell_barcode like Sample (source of cell_barcode)
anndata	Annotation dataframe. It consist of information such as Sample (sample name), PTID (donor/participant), Time (longitudinal timepoints)

Value

PALMO object with scRNA

Examples

## Not run: 
palmo_obj=createPALMOfromsinglecellmatrix(counts, metadata, annotation)

## End(Not run)

aifimmunology/PALMO documentation built on Oct. 21, 2022, 7:39 p.m.