New cell count set

Create a new cell_data_set object.

new_cell_count_set(
  cds,
  sample_group,
  cell_group,
  sample_metadata = NULL,
  cell_metadata = NULL,
  lower_threshold = NULL,
  upper_threshold = NULL,
  keep_cds = TRUE,
  norm_method = c("size_factors", "TSS", "CSS", "RLE", "GMPR", "Wrench", "none"),
  size_factors = NULL,
  pseudocount = 0
)

Arguments

cds

A Monocle cell data set object.

sample_group

A column in colData(cds) that specifes how cells are grouped into samples.

cell_group

A column in colData(cds) that specifies how cells are grouped into types or states (e.g. cluster).

sample_metadata

Data frame containing attributes of individual samples, where the column named 'sample' has entries in sample_group.

cell_metadata

Data frame containing attributes of individual cell groups, where row.names(cell_metadata) are entries in cell_group

lower_threshold

numeric Minimum number of cells in retained cell_groups.

upper_threshold

numeric Maximum number of cells in retained cell_groups.

norm_method

string Normalization method used to compute scaling factors used as offset during PLN inference.

size_factors

numeric vector or matrix User supplied vector or matrix of offsets passed the PLNmodels::prepare_data() method.

Value

a new cell_data_set object