PALMO (version 0.1.2)

avgExpCalc: 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)

Value

PALMO object with avg expression

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'

Examples

if (FALSE) {
palmo_obj=avgExpCalc(data_object=palmo_obj, assay='RNA',
group_column='celltype')
}