get_norm_ref: Normalizes cell type profiles to a target dataset

In dmcable/RCTD: SpatialeXpressionR: Cell type identification and cell type-specific differential expression in spatial transcriptomics

Normalizes cell type profiles to a target dataset

Description

renormalizes cell_type_means to have average the same as the puck. The average for each gene is weighted by cell type proportions given by proportions.

Usage

get_norm_ref(puck, cell_type_means, gene_list, proportions)

Arguments

puck	an object of type SpatialRNA, the target dataset
cell_type_means	a data_frame (genes by cell types) for mean normalized expression (see get_cell_type_info)
gene_list	a list of genes to be used for the normalization
proportions	a named list (for each cell type) of proportion of the cell type on the bulk dataset (not constrained to sum to 1)

Value

Returns cell_type_means, a data_frame (genes by cell types) for mean normalized cell type expression profiles in which platform effects have been removed to match the SpatialRNA data.

dmcable/RCTD documentation built on Feb. 24, 2024, 11:03 p.m.