pseudobulk | R Documentation |
Sum up cells in count matrix raw
for bulk RNA methods such as
DESeq2.
pseudobulk(raw, pseudobulk_id)
raw |
A matrix with raw UMI counts, cells in columns. |
pseudobulk_id |
A factor that identifies which cells should go to which pseudobulk. Generate pseudobulk_ids with the pseudobulk_id function! |
A matrix where each column is a pseudobulk and each row a gene.
# 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).
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