Collate Lymphgen. — collate_lymphgen • GAMBLR

Expand a sample_table (metadata) horizontally with different flavours of lymphgen data.

collate_lymphgen(
  these_samples_metadata,
  lymphgen_version = "default",
  tidy = FALSE
)

Arguments

these_samples_metadata: Optional parameter with metadata filtered for sample_ids of interest. If provided, this function will join lymphgen with this metadata, regardless of tidy TRUE/FALSE.
lymphgen_version: Version of selected lymphgen, default is "default".
tidy: Boolean parameter, set to TRUE for tidy format (i.e long format with no columns dropped). Default is FALSE, which returns the data in a wide format, keeping both the original Subtype. Prediction and tidied LymphGen values and puts the values from each "flavour" in its own column.

Value

A df with lymphgen information.

Details

This function takes a sample table (metadata) and adds different flavours of lymphgen data. It is possible to call this function with an already subset metadata table (with sample IDs of interest) with these_samples_metadata. If this is done, the function will join the lymphgen data with this table. Currently, the only supported lymphgen_version is "default". For more information refer to the function examples.

Examples

this_meta = get_gambl_metadata()
dlbcl_meta = dplyr::filter(this_meta, pathology == "DLBCL")

wide_lymphgen = collate_lymphgen(these_samples_metadata = dlbcl_meta,
                                 lymphgen_version = "default",
                                 tidy = FALSE)
#> Joining with `by = join_by(sample_id)`