summarize_scd_clusters: Summarize scores across observed clusters in a scd.

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

Summarize scores across observed clusters in a scd.

Description

Currently this assumes the set of outputs produced by Seurat's AddModuleScore() for a gsc. It summarizes those scores for each cluster and gives back the mean, sd, and z.

Usage

summarize_scd_clusters(
  scd,
  fx = "mean",
  column_prefix = "descartes",
  column_range = NULL,
  cluster_column = "cluster_sample",
  real_column_names = NULL,
  abbreviate = TRUE,
  min_mean = NULL
)

Arguments

scd	Input dataset.
fx	Function to summarize, this may change.
column_prefix	Prefix for the scores of interest.
column_range	Explicitly set the range of interested columns.
cluster_column	The column containing the information about cluster occupancy.
real_column_names	The original columns get names like bob1 to bobn, this can be used to make them more informative.
abbreviate	When using mSigDB information, the category names are exceedingly long with often a consistent prefix.
min_mean	Currently unused, but intended to filter out gsc which are not observed to any significant degree.

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