read_10x: Read 10x data and generate scNMF object

In hjunwoo/ccfindR: Cancer Clone Finder

Description

Read count, gene, and barcode annotation data in 10x format and create an object of class scNMFSet.

Usage

read_10x(dir, count = "matrix.mtx", genes = "genes.tsv",
  barcodes = "barcodes.tsv", remove.zeros = TRUE)

Arguments

dir	Name of directory containing data files.
count	Name of count matrix file.
genes	Name of gene annotation file.
barcodes	Name of cell annotation file.
remove.zeros	If TRUE, empty rows/columns are removed.

Details

Files for count, genes, and barcodes are assumed to be present in dir. Count data are in sparse "Matrix Market" format (https://math.nist.gov/MatrixMarket/formats.html).

Value

Object of class scNMFSet

Examples

library(S4Vectors)
s <- scNMFSet(count=matrix(rpois(n=12,lambda=3),4,3))
rowData(s) <- DataFrame(seq_len(4))
colData(s) <- DataFrame(seq_len(3))
write_10x(s,dir='.')
s <- read_10x(dir='.')
s

hjunwoo/ccfindR documentation built on Oct. 4, 2019, 10:31 a.m.