get10Xmatrix — get10Xmatrix • Giotto

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

get10Xmatrix(
  path_to_data,
  gene_column_index = 1,
  remove_zero_rows = TRUE,
  split_by_type = 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
split_by_type: split into multiple matrices based on 3rd column of features.tsv(.gz)

Value

sparse expression matrix from 10X

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.