Gitlab Community Edition Instance

Skip to content

Add functionality to summarize samples/features

Use case / idea

Often, users would like to obtain summary values, like the median, mean, max or min of a sample/feature statistic. Such functionality can easily implemented for SingleCellExperiment and Seurat objects. This data can be put in a table like below:

Statistic min max median
total features 849 4155 2312
total counts 10500 1249871 505012

Example

  • A user wants to know what the median number of detected features is for all samples.
  • A user wants to know the minimum number of cells all features are detected in.

Previous work

For my static PDF report, such functionality exists. I'll paste the code below.

Task / Goal

  1. Create a function to summarize samples of a SingleCellExperiment or Seurat object, using given summary functions and statistics.
  2. Create a function to summarize features of a SingleCellExperiment or Seurat object, using given summary functions and statistics.

Extensions

  1. Enable grouping by a factor in the functions above.