get10Xmatrix: get10Xmatrix

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

Description

This function creates an expression matrix from a 10X structured folder

Usage

get10Xmatrix(path_to_data, gene_column_index = 1)

Arguments

path_to_data	path to the 10X folder
gene_column_index	which column from the features or genes .tsv file to use for row ids

Details

A typical 10X folder is named raw_feature_bc_matrix or raw_feature_bc_matrix and tt has 3 files:

• barcodes.tsv(.gz)

• features.tsv(.gz) or genes.tsv(.gz)

• matrix.mtx(.gz)

By default the first column of the features or genes .tsv file will be used, however if multiple annotations are provided (e.g. ensembl gene ids and gene symbols) the user can select another column.

Value

sparse expression matrix from 10X

bernard2012/Giotto documentation built on Sept. 22, 2020, 10:29 a.m.