create_scd: Create a combined seurat object from a sample sheet.

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Create a combined seurat object from a sample sheet.

Description

I would like to have a simpler function for creating seurat data structures similar to my create_expt(). This will try to do so.

Usage

create_scd(
  metadata,
  expression_column = "gexfile",
  vdj_t_column = "vdjtcells",
  vdj_b_column = "vdjbcells",
  prefix = NULL,
  separate = FALSE,
  types = "gex",
  mito_pattern = "^mt-",
  ribo_pattern = "^Rp[sl]"
)

Arguments

metadata	Sample sheet.
expression_column	Metadata column containing the base location of the cellranger outputs.
vdj_t_column	Column, which if filled in, tells this to look for VDJ information specific to light chains.
vdj_b_column	Column, which if filled in, tells this to look for VDJ information specific to heavy chains.
prefix	Arbitrary prefix for the location information, included because I am messing with cellranger and have multiple output directories and want to be able to switch between them.
separate	When true, this function should return a list comprised of the individual sample objects.
types	Types of data to add to the scd.
mito_pattern	Pattern used to find mitochondrial genes.
ribo_pattern	Pattern used to find ribosomal proteins.

Value

Either a list or merged seurat object(s).

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.