record_seurat_samples: Add into the miscellaneous SCD slot a dataframe with some...

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Add into the miscellaneous SCD slot a dataframe with some summary stats.

Description

There are some simple summaries which are nice to have on hand regarding the number of RNAs, cells, rProteins, rmito observed. This function collects them and drops them into a dataframe within the slot 'misc' of the SCD. I may also print to screen some pretty skims of the results.

Usage

record_seurat_samples(
  scd,
  type = "num_cells",
  pattern = NULL,
  column_name = NULL,
  column_prefix = NULL,
  verbose = FALSE,
  group = "Idents",
  assay = "RNA"
)

Arguments

scd	Single Cell Dataset to query.
type	Type of column to add to the metadata df, named for the column in the Cell-annotation table to query.
pattern	Pattern used for regex-based queries.
column_name	Name for the new column.
column_prefix	Prefix added to the new column.
verbose	Print the summaries to screen?
group	Could up the data by this column.
assay	Use this assay. (might be useful if you have antibody data)

Value

Give back the SCD with some new information.

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.