pseudobulk_id: Generate unique IDs to identify your pseudobulks.

In cellpypes: Cell Type Pipes for Single-Cell RNA Sequencing Data

Generate unique IDs to identify your pseudobulks.

Description

This function generates unique IDs that are valid colnames as well. Use these IDs in function pseudobulk.

Usage

pseudobulk_id(factor_df)

Arguments

factor_df

Data frame where each column helps to identify a pseudobulk. Each row in factor_df corresponds to a single cell in your raw count matrix. Typical columns of factor_df are for example patient, treatment and cell type – anything that uniquely identifies a replicate.

Details

Wraps make.names to generate syntactically valid IDs. Use these IDs in the pseudobulk function. Note that this function combines all columns in factor_df, so only include the columns that uniquely identify replicates. Cells from the same experimental unit

Value

Factor with syntactically valid and unique IDs.

Examples

# Create pseudobulk counts and coldata for DESeq2: 
coldata <- data.frame(
  celltype = rep(c("X+Y-", "X+Y+", "X-Y+", "X-Y-"),
                 each = nrow(simulated_umis$embed)/4), # 4 cell types
  patient  = c("3", "500.", "*5", "/")
)
coldata$pseudobulk_id <- pseudobulk_id(coldata)
counts <- pseudobulk(simulated_umis$raw, coldata$pseudobulk_id)
# Use counts/coldata as input for DESeqDataSetFromMatrix (DESeq2).

cellpypes documentation built on May 29, 2024, 1:24 a.m.