Get a pseudobulk of bins with at least 2 replicates
get_bins_as_bulk.RdThis function will try to create a pseudobulked count matrix for the bins. When a replicate has too few cells, it is discounted. If only one exists, then we sample from it twice to create the pseudobulks.
Examples
library(SingleCellExperiment, quietly = TRUE)
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library(blase)
counts <- matrix(rpois(1000, lambda = 10), ncol = 100, nrow = 10)
sce <- SingleCellExperiment::SingleCellExperiment(
assays = list(normcounts = counts, counts = counts / 2)
)
sce$pseudotime <- seq_len(100) - 1
colnames(sce) <- seq_len(100)
rownames(sce) <- as.character(seq_len(10))
sce <- assign_pseudotime_bins(sce,
n_bins = 5,
pseudotime_slot = "pseudotime", split_by = "cells"
)
sce$replicate <- rep(c(1, 2), 50)
result <- get_bins_as_bulk(
sce,
min_cells_for_bulk = 1,
replicate_slot = "replicate"
)
result
#> bin_1_rep_1 bin_1_rep_2 bin_2_rep_1 bin_2_rep_2 bin_3_rep_1 bin_3_rep_2
#> 1 45.0 51.5 48.0 48.0 56.5 47.5
#> 10 49.5 50.5 51.5 52.5 39.5 54.5
#> 2 44.5 50.5 47.0 55.0 44.5 46.5
#> 3 53.5 50.0 49.0 58.5 57.5 54.0
#> 4 60.0 54.5 55.5 58.0 49.0 61.5
#> 5 46.0 48.5 50.5 48.5 56.0 44.0
#> 6 54.0 49.5 56.5 51.0 47.5 46.5
#> 7 39.0 49.0 54.0 44.5 50.5 51.5
#> 8 43.0 46.5 45.0 41.5 52.0 54.5
#> 9 50.5 52.0 50.5 51.0 42.0 43.0
#> bin_4_rep_1 bin_4_rep_2 bin_5_rep_1 bin_5_rep_2
#> 1 57.5 52.5 51.5 44.5
#> 10 61.5 50.0 49.0 38.0
#> 2 45.0 46.0 53.0 56.5
#> 3 45.5 52.0 52.5 55.0
#> 4 50.0 50.5 50.5 50.0
#> 5 50.0 54.0 50.0 48.5
#> 6 55.0 47.5 51.0 49.5
#> 7 52.0 55.0 54.0 57.5
#> 8 50.5 39.0 50.0 44.5
#> 9 47.5 49.0 45.0 52.5