get10Xmatrix: get10Xmatrix

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

get10Xmatrix

Description

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

Usage

get10Xmatrix(path_to_data, gene_column_index = 1, remove_zero_rows = TRUE)

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
remove_zero_rows	removes rows with sum equal to zero

Details

A typical 10X folder is named raw_feature_bc_matrix or filtered_feature_bc_matrix and it 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

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.