process_counts_hash: Processes counts into a Seurat object prepared for alignment.

In Chris-Cherry/sctools: Single cell analysis tools package

Description

This script reads in a counts file from either the DropSeq or 10x pipeline, converts the genes to a given naming convention (MGI or HGNC) and creates Seurat object from counts. It is the input for align_sers. This file also adds hashing information to a Seurat object and adds hash id to barcodes.

Usage

process_counts_hash(
  directory,
  from_gene,
  to_gene,
  hash_dir = NULL,
  hash_meta = NULL,
  sample_id = NULL,
  type = "DropSeq",
  T_dir = NULL,
  B_dir = NULL,
  umi_thresh = 500
)

Arguments

directory	directory containing the output files of align_dropseq_2.sh or cell ranger
from_gene	"ENSG" or "ENSMUSG" or "HGNC" or "MGI"
to_gene	"MGI" or "HGNC"
hash_dir	Directory containing hash counts files
hash_meta	csv file containing conversion of hash ID to sample name
sample_id	Optional experimental ID to prefix cell names
type	"DropSeq" or "10x"
T_dir	Optional directory to T cell TCR
B_dir	optional directory to B cell BCR
umi_thresh	Minimum total umi count for cells

Value

Outputs a Seurat file prepared to rPCA anchoring

Chris-Cherry/sctools documentation built on Jan. 25, 2022, 2:19 p.m.