importdata: importdata

In hemberg-lab/sctransfermap: sctransfermap for predicting cell type in single-cell data (RNA-seq and ATAC-seq)

Description

importdata will import sc-data (scRNA-seq or scATAC-seq) and make gene(peak)-by-cell matrix

Usage

importdata(file, opt = "raw", datatype = "RNAseq",
  colname_file = FALSE, rowname_file = FALSE, row_opt = 1)

Arguments

file	file of the single-cell data (ex: scRNA-seq, scATAC-seq)
opt	data format of the single-cell data raw: tab-delimited text file SingleCellExperiment: SingleCellExperiment rds file sparse: MatrixMarket format (written by writeMM)
datatype	"RNAseq" or "atac"
colname_file	colname_file for sparse matrix (usually cell name), when opt is "sparse". Otherwise, it is FALSE
rowname_file	rowname_file for sparse matrix (gene name: official gene symbol or peak location), when opt is "sparse". Otherwise, it is FALSE
row_opt	indicates the column number that sholud be used for the gene(peak) name

Value

a matrix class composed of gene/peak_location(row)-by-cell(column)

Examples

data <- importdata("filename")
- scRNA-seq with raw matrix file
data <- importdata("sparse matrix file name", opt = "sparse", colname_file = "cell file", rowname_file = "row_file")
- for sparse matrix file

hemberg-lab/sctransfermap documentation built on Nov. 11, 2019, 6:23 a.m.