avgExpCalc: avgExpCalc Function

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

avgExpCalc Function

Description

This function allows you to calculate average gene expression on log-normalized data by group defined by user. This function uses Seurat function AverageExpression (https://satijalab.org/seurat/reference/averageexpression)

Usage

avgExpCalc(data_object, assay = "RNA", group_column)

Arguments

data_object	Input PALMO S4 object. Contains annotation table and expression matrix or data frame. Rows represent gene/proteins column represents participant samples (same as annotation table Sample column)
assay	Single cell data Assay type ('RNA', 'SCT'). Default 'RNA'
group_column	Calculate average expression by given group like 'celltype' or 'cluster'

Value

PALMO object with avg expression

Examples

## Not run: 
palmo_obj=avgExpCalc(data_object=palmo_obj, assay='RNA',
group_column='celltype')

## End(Not run)

PALMO documentation built on Aug. 18, 2022, 1:06 a.m.