createPALMOobject: createPALMOobject Function

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

createPALMOobject Function

Description

This function allows to create PALMO object using Annotation dataframe and Data dataframe. The Data can be bulk data or single cell data. The bulk input data should consists of rows as genes/proteins/features and column as Sample name (same as user-defined Samples in Annotation dataframe). The single cell data should be Seurat object (please check https://search.r-project.org/CRAN/refmans/SeuratObject/html/CreateSeuratObject.html). In case Seurat object not available then user can use function createPALMOfromsinglecellmatrix to create PALMO object. The Seurat object/metadata should have Sample column corresponding to Annotation dataframe.

Usage

createPALMOobject(anndata, data)

Arguments

anndata	Annotation dataframe. It consist of information such as Sample (sample name), PTID (donor/participant), Time (longitudinal timepoints)
data	Data can be bulk data or single cell data

Value

PALMO S4 object

Examples

## Not run: 
palmo_obj=createPALMOobject(anndata, data)

## End(Not run)

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