df2SCE: Exporting a dataframe to SingleCellObject

In biosurf/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,
  scatter = NULL,
  clean_names = FALSE,
  sample_col = "sample",
  panel = NULL,
  panel_channel = "Channel",
  panel_antigen = "Marker",
  panel_type = NULL,
  transform_cofactor = 5
)

Arguments

df	Tibble with expression values and metadata
markers	Markers to include in exprs and counts 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	It is the column name in the df that contains the sample names. Defaults to 'sample'.
panel	Optional: Panel as a data.frame. Should have colnames Channel, Marker, Type unless otherwise specified in the panel_ args. Should be included if you want to store FCS files
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. Set to NULL to disregard.
transform_cofactor	The cofactor to use when reverse-transforming to raw counts

See Also

Other export: sce2FCS()

Examples

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

biosurf/cyCombine documentation built on May 23, 2024, 4:07 a.m.