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Create an ScPeaks object from an ScCounts object

Source: R/ScCounts.R
scc_to_peaks.Rd

given an ScCounts object and peaks, summarise the counts over the peaks and return a ScPeaks object

Usage

scc_to_peaks(
  sc_counts,
  peaks,
  cells = NULL,
  metadata = NULL,
  mc_size_eps_q = 0.1
)

Arguments

sc_counts

a ScCounts object

peaks

a data frame with the peak intervals (chrom, start, end) and a column called "peak_name"

cells

names of cells to include. Default: all cells.

metadata

(optional) per-metacell metadata. A data frame with a column called 'metacell' and additional metacell annotations.

mc_size_eps_q

(optional) quantile of MC size (in UMIs) to scale the number of UMIs per metacell. \(egc_ij\) would then be the fraction of peak i in metacell j multiplied by the mc_size_eps_q quantile of metacell sizes.

Value

a McPeaks object

Examples

if (FALSE) {
atac_sc <- import_from_10x("pbmc_data", genome = "hg38")
sc_counts <- scc_read("pbmc_reads")
atac_sc <- scc_to_peaks(sc_counts, atac_sc@peaks)
}