pseudobulk_id {cellpypes}

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).