LoadData: Load sequencing data and annotations

In mkarikom/RSoptSC: Low-Rank Factorization for Subspace-clustering

Load sequencing data and annotations

Description

A matrix of counts with rows as genes and columns as cells must be provided. Gene and cell ids are provided in separate text files. For labeled data, the vector must be provided as a separate file. The counts are loaded as a sparse matrix, the other values as character vectors.

Usage

LoadData(d_f, gene_f, cell_f, annotation_f)

Arguments

d_f	path to the file containing counts
gene_f	path the file containing unique gene ids
cell_f	path the file containing unique cell ids
annotation_f	path to the file containing labels, e.g. tissue type of the cells

Value

a list containing:

cell_names	cell ids
gene_names	eg gene symbols
data	counts matrix
annotation	cell labels

mkarikom/RSoptSC documentation built on May 10, 2023, 1:10 a.m.