txReadDGE: Read in Digital Gene Expression Matrix from 10X Cellranger

In farrellja/URD: URD

Description

Read in Digital Gene Expression Matrix from 10X Cellranger

Usage

txReadDGE(
  output.path,
  dge.name = NULL,
  cells.read = NULL,
  name.by = c("gene", "id"),
  strip.num = T
)

Arguments

output.path	(Character) Path that contains barcodes.tsv, genes.tsv, and matrix.mtx from Cellranger
dge.name	(Character) Name to append to all cell barcodes if multiple tables will be combined (default: NULL)
cells.read	(Character vector) Cell names to trim the matrix to, if desired (will be matched after strip.num, before appending dge.name)
name.by	(Character: "gene" or "id") Whether to name genes by gene ID, or gene name. If gene name, expression of gene IDs with the same name will be summed.
strip.num	(Logical) Cellranger appends a batch number (e.g. "-1") to cell barcodes. If TRUE, this strips it away.

Value

A dgCMatrix, where rows are genes and columns are cells.

farrellja/URD documentation built on June 17, 2020, 4:48 a.m.