df2SCE: Exporting a dataframe to SingleCellObject

In shdam/cyCombine: Robust integration of single-cell cytometry datasets within and across technologies

Exporting a dataframe to SingleCellObject

Description

Conversion of dataframe into separate data and metadata objects for subsequent transformation. Rename variable names to fit the requirements of SCE-based tools

Usage

df2SCE(
  df,
  markers = NULL,
  non_markers = NULL,
  sample_col = "sample",
  panel = NULL,
  panel_channel = "Channel",
  panel_antigen = "Marker",
  panel_type = "Type"
)

Arguments

df	Tibble with expression values and metadata
markers	Markers to include in exprs object of SCE. If NULL, markers will be found using the get_markers function.
non_markers	Non-markers to include as colData in SCE. If NULL, non_markers will be based on cyCombine::non_markers.
sample_col	The name of the column containing sample IDs
panel	Optional: Panel as a data.frame. Should have colnames Channel, Marker, Type unless otherwise specified in the panel_ args.
panel_channel	Optional: Only used if panel is given. It is the column name in the panel data that contains the channel names
panel_antigen	Optional: Only used if panel is given. It is the column name in the panel data that contains the antigen names
panel_type	Optional: Only used if panel is given. It is the column name in the panel data that contains the antigen types (none, state, type). "none" will be excluded from SCE.

Examples

## Not run: 
sce <- df %>%
  df2SCE(markers = markers, non_markers = NULL, panel = panel)
  
## End(Not run)

shdam/cyCombine documentation built on June 12, 2022, 11:29 p.m.