ReadNanostring: Read and Load Nanostring SMI data

In Seurat: Tools for Single Cell Genomics

Read and Load Nanostring SMI data

Description

Read and Load Nanostring SMI data

Usage

ReadNanostring(
  data.dir,
  mtx.file = NULL,
  metadata.file = NULL,
  molecules.file = NULL,
  segmentations.file = NULL,
  type = "centroids",
  mol.type = "pixels",
  metadata = NULL,
  mols.filter = NA_character_,
  genes.filter = NA_character_,
  fov.filter = NULL,
  subset.counts.matrix = NULL,
  cell.mols.only = TRUE
)

LoadNanostring(data.dir, fov, assay = "Nanostring")

Arguments

data.dir	Path to folder containing Nanostring SMI outputs
mtx.file	Path to Nanostring cell x gene matrix CSV
metadata.file	Contains metadata including cell center, area, and stain intensities
molecules.file	Path to molecules file
segmentations.file	Path to segmentations CSV
type	Type of cell spatial coordinate matrices to read; choose one or more of: “centroids”: cell centroids in pixel coordinate space “segmentations”: cell segmentations in pixel coordinate space
mol.type	Type of molecule spatial coordinate matrices to read; choose one or more of: “pixels”: molecule coordinates in pixel space
metadata	Type of available metadata to read; choose zero or more of: “Area”: number of pixels in cell segmentation “fov”: cell's fov “Mean.MembraneStain”: mean membrane stain intensity “Mean.DAPI”: mean DAPI stain intensity “Mean.G”: mean green channel stain intensity “Mean.Y”: mean yellow channel stain intensity “Mean.R”: mean red channel stain intensity “Max.MembraneStain”: max membrane stain intensity “Max.DAPI”: max DAPI stain intensity “Max.G”: max green channel stain intensity “Max.Y”: max yellow stain intensity “Max.R”: max red stain intensity
mols.filter	Filter molecules that match provided string
genes.filter	Filter genes from cell x gene matrix that match provided string
fov.filter	Only load in select FOVs. Nanostring SMI data contains 30 total FOVs.
subset.counts.matrix	If the counts matrix should be built from molecule coordinates for a specific segmentation; One of: “Nuclear”: nuclear segmentations “Cytoplasm”: cell cytoplasm segmentations “Membrane”: cell membrane segmentations
cell.mols.only	If TRUE, only load molecules within a cell
fov	Name to store FOV as
assay	Name to store expression matrix as

Value

ReadNanostring: A list with some combination of the following values:

• “matrix”: a sparse matrix with expression data; cells are columns and features are rows

• “centroids”: a data frame with cell centroid coordinates in three columns: “x”, “y”, and “cell”

• “pixels”: a data frame with molecule pixel coordinates in three columns: “x”, “y”, and “gene”

LoadNanostring: A Seurat object

Progress Updates with progressr

This function uses progressr to render status updates and progress bars. To enable progress updates, wrap the function call in with_progress or run handlers(global = TRUE) before running this function. For more details about progressr, please read vignette("progressr-intro")

Parallelization with future

This function uses future to enable parallelization. Parallelization strategies can be set using plan. Common plans include “sequential” for non-parallelized processing or “multisession” for parallel evaluation using multiple R sessions; for other plans, see the “Implemented evaluation strategies” section of ?future::plan. For a more thorough introduction to future, see vignette("future-1-overview")

Note

This function requires the data.table package to be installed

Seurat documentation built on Nov. 18, 2023, 1:10 a.m.