rliger (version 1.0.0)

read10X: Read 10X alignment data (including V3)

Description

This function generates a sparse matrix (genes x cells) from the data generated by 10X's cellranger count pipeline. It can process V2 and V3 data together, producing either a single merged matrix or list of matrices. Also handles multiple data types produced by 10X V3 (Gene Expression, Antibody Capture, CRISPR, CUSTOM).

Usage

read10X(
  sample.dirs,
  sample.names,
  merge = TRUE,
  num.cells = NULL,
  min.umis = 0,
  use.filtered = FALSE,
  reference = NULL,
  data.type = "rna",
  verbose = TRUE
)

Arguments

sample.dirs

List of directories containing either matrix.mtx(.gz) file along with genes.tsv, (features.tsv), and barcodes.tsv, or outer level 10X output directory (containing outs directory).

sample.names

Vector of names to use for samples (corresponding to sample.dirs)

merge

Whether to merge all matrices of the same data type across samples or leave as list of matrices (default TRUE).

num.cells

Optional limit on number of cells returned for each sample (only for Gene Expression data). Retains the cells with the highest numbers of transcripts (default NULL).

min.umis

Minimum UMI threshold for cells (default 0).

use.filtered

Whether to use 10X's filtered data (as opposed to raw). Only relevant for sample.dirs containing 10X outs directory (default FALSE).

reference

For 10X V<3, specify which reference directory to use if sample.dir is outer level 10X directory (only necessary if more than one reference used for sequencing). (default NULL)

data.type

Indicates the protocol of the input data. If not specified, input data will be considered scRNA-seq data (default 'rna', alternatives: 'atac').

verbose

Print messages (TRUE by default)

Value

List of merged matrices across data types (returns sparse matrix if only one data type detected), or nested list of matrices organized by sample if merge=F.

Examples

# NOT RUN {
# 10X output directory V2 -- contains outs/raw_gene_bc_matrices/<reference>/...
sample.dir1 <- "path/to/outer/dir1"
# 10X output directory V3 -- for two data types, Gene Expression and CUSTOM
sample.dir2 <- "path/to/outer/dir2"
dges1 <- read10X(list(sample.dir1, sample.dir2), c("sample1", "sample2"), min.umis = 50)
ligerex <- createLiger(expr = dges1[["Gene Expression"]], custom = dges1[["CUSTOM"]])
# }