sce_int_processed_fn: Subset each object in a list of 'SingleCellExperiment'...

In bioinfocz/scdrake: A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

Subset each object in a list of SingleCellExperiment objects to common data and their corresponding metadata (e.g. HVGs).

Description

This will subset all SingleCellExperiment objects to common:

• Features and HVGs (whose data are saved in metadata).

• Column data (colData()). Columns starting with "cluster_" will be renamed to "cluster_<batch>", e.g. "cluster_sc3_3_pbmc1k".

Usage

sce_int_processed_fn(sce_int_raw)

Arguments

sce_int_raw

(input target) A named list of SingleCellExperiment objects.

Value

A list of SingleCellExperiment objects. Output target: sce_int_processed

The following items of metadata() of each SingleCellExperiment object are added or modified:

• hvg_ids, hvg_metric_fit: subsetted to common features.

• n_features_orig: an integer scalar: number of features (rows) before subsetting to common space.

bioinfocz/scdrake documentation built on Sept. 19, 2024, 4:43 p.m.