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Create a ScMaSigPro object from counts and cell metadata

Source: R/create_scmp.R
create_scmp.Rd

create_scmp() creates a ScMaSigPro object from a count matrix and a table of cell metadata with the pseudotime and the path of each cell, such as the result of assign_paths(). Bins made elsewhere can be given too.

Usage

create_scmp(
  counts,
  cell_data,
  feature_data = NULL,
  bin_counts = NULL,
  bin_cell_data = NULL,
  ptime_col,
  path_col,
  use_as_bin = FALSE
)

Arguments

counts

A matrix of raw counts, genes by cells.

cell_data

A data frame of cell metadata, one row per column of counts, named like them.

feature_data

An optional data frame of gene metadata, one row per gene of counts, named like them or with automatic row names. It becomes the rowData() of the Sparse slot, and of the Dense slot when this function builds it.

bin_counts

Optional pseudo-bulk counts of bins made outside scMaSigPro: a matrix with the genes of counts as rows, in the same order, and one column per bin. Needs bin_cell_data; not with use_as_bin = TRUE.

bin_cell_data

A data frame with one row per bin, named like the columns of bin_counts, with the binned pseudotime in ptime_col and the path in path_col. A scmp_bin_size column gives the number of cells of each bin; without it the sizes are NA.

ptime_col

The name of the column of the cell metadata that holds the pseudotime of each cell.

path_col

The name of the column of the cell or bin metadata that holds the path label of each cell or bin.

use_as_bin

Whether every cell is a bin of its own, without pseudo-bulking, as for bulk time-course data.

Value

A ScMaSigPro object with the cells in the Sparse slot and, with use_as_bin = TRUE or bin_counts, the bins in the Dense slot.

Details

By default the Dense slot is empty and sc.squeeze() bins the cells. With use_as_bin = TRUE every cell is a bin. With bin_counts and bin_cell_data it holds bins made outside scMaSigPro and the workflow continues with sc.set.poly(); such bins have no member cells, so pb_counts() and sc.restruct() do not apply.

See also

Other input helpers: as_scmp(), assign_paths(), paths_from_graph()

Author

Priyansh Srivastava spriyansh29@gmail.com

Examples

data("splat.sim", package = "scMaSigPro")
counts <- SummarizedExperiment::assay(splat.sim, "counts")
cells <- as.data.frame(SummarizedExperiment::colData(splat.sim))
scmp <- create_scmp(counts, cells, ptime_col = "Step", path_col = "Group")
scmp
#> Class: ScMaSigProClass
#> nCells: 200
#> nFeatures: 100
#> Pseudotime Range: 1 100
#> Branching Paths: Path2, Path1