Import-10X-mtx: Import data from 10X Genomics output (tsv-mtx).

In bioinfoDZ/RISC: Robust Integration of Single-Cell RNA-Seq Datasets

Import data from 10X Genomics output (tsv-mtx).

Description

Import data directly from 10X Genomics output, usually using filtered gene matrices which contains three files: matrix.mtx, barcode.tsv and gene.tsv. The user only need to input the directory into "data.path". If not the original 10X Genomics output, the user have to make sure the barcode.tsv and gene.tsv without col.names, the barcode.tsv at least contains one column for cell barcode, and the gene.tsv has two columns for gene Ensembl ID and Symbol.

Usage

read10X_mtx(data.path, sep = "\t", is.filter = TRUE)

Arguments

data.path	Directory containing the filtered 10X Genomics output, including three files: matrix.mtx, barcode.tsv (without colnames) and gene.tsv (without colnames).
sep	The sep can be changed by the users
is.filter	Remove not expressed genes.

Value

RISC single cell dataset, including count, coldata, and rowdata.

bioinfoDZ/RISC documentation built on March 30, 2024, 9:19 p.m.