construct_pseudobulk: Construct sample-level pseudobulk gene expression matrix

In byzhang23/TreeCorTreat: Tree-based correlation screen for phenotype-associated transcriptomic features and cell types

Construct sample-level pseudobulk gene expression matrix

Description

This function takes in raw count gene expression matrix and cell-level metadata as inputs, and generates sample-level normalized pseudobulk gene expression matrix.

Usage

construct_pseudobulk(expr, cell_meta, filter_prop = 0.1)

Arguments

expr	A raw count gene expression matrix
cell_meta	A data frame for cell-level metadata, where each row is a cell. Must contain these columns: barcode, celltype and sample.
filter_prop	A number ranges from 0 to 1, to filter low expressed genes across samples (by default: 0.1). Genes with at least this proportion of samples with log2-normalized count greater than 0.01 are retained.

Value

A sample-level normalized pseudobulk gene expression matrix with genes in the row and samples in the columns

Author(s)

Boyang Zhang <[e-mail]>, Hongkai Ji

Examples

## Not run: 
# default
construct_pseudobulk(expr,cell_meta)
# retain all genes
construct_pseudobulk(expr,cell_meta,filter_prop = 0)

## End(Not run)

byzhang23/TreeCorTreat documentation built on May 7, 2024, 8:37 a.m.