get10Xmatrix#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/general_help.R#L919

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#

Argument

Description

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