runspatialdecon,NanoStringGeoMxSet-method {SpatialDecon}R Documentation

Run spatialdecon on a NanostringGeomxSet object

Description

A wrapper for applying spatialdecon to a NanostringGeomxSet object.

Usage

## S4 method for signature 'NanoStringGeoMxSet'
runspatialdecon(
  object,
  X = NULL,
  norm_elt = NULL,
  raw_elt = NULL,
  wts = NULL,
  resid_thresh = 3,
  lower_thresh = 0.5,
  align_genes = TRUE,
  is_pure_tumor = NULL,
  n_tumor_clusters = 10,
  cell_counts = NULL,
  cellmerges = NULL,
  maxit = 1000
)

Arguments

object

A NanostringGeomxSet object.

X

Cell profile matrix. If NULL, the safeTME matrix is used.

norm_elt

normalized data element in assayData

raw_elt

raw data element in assayData

wts

Optional, a matrix of weights.

resid_thresh

A scalar, sets a threshold on how extreme individual data points' values can be (in log2 units) before getting flagged as outliers and set to NA.

lower_thresh

A scalar. Before log2-scale residuals are calculated, both observed and fitted values get thresholded up to this value. Prevents log2-scale residuals from becoming extreme in points near zero.

align_genes

Logical. If TRUE, then Y, X, bg, and wts are row-aligned by shared genes.

is_pure_tumor

A logical vector denoting whether each AOI consists of pure tumor. If specified, then the algorithm will derive a tumor expression profile and merge it with the immune profiles matrix.

n_tumor_clusters

Number of tumor-specific columns to merge into the cell profile matrix. Has an impact only when is_pure_tumor argument is used to indicate pure tumor AOIs. Takes this many clusters from the pure-tumor AOI data and gets the average expression profile in each cluster. Default 10.

cell_counts

Number of cells estimated to be within each sample. If provided alongside norm_factors, then the algorithm will additionally output cell abundance esimtates on the scale of cell counts.

cellmerges

A list object holding the mapping from beta's cell names to combined cell names. If left NULL, then defaults to a mapping of granular immune cell definitions to broader categories.

maxit

Maximum number of iterations. Default 1000.

Value

if not given cellmerges and cell_counts, a valid GeoMx S4 object including the following items

if given cellmerges, the valid GeoMx S4 object will additionally include the following items

if given cell_counts, the valid GeoMx S4 object will additionally include the following items

if given both cellmerges and cell_counts, the valid GeoMx S4 object will additionally include the following items

Examples


library(GeomxTools)
datadir <- system.file("extdata", "DSP_NGS_Example_Data", package = "GeomxTools")
demoData <- readRDS(file.path(datadir, "/demoData.rds"))

demoData <- shiftCountsOne(demoData)
target_demoData <- aggregateCounts(demoData)

target_demoData <- normalize(target_demoData, "quant")

demoData <- runspatialdecon(object = target_demoData, 
                            norm_elt = "exprs_norm",
                            raw_elt = "exprs")


[Package SpatialDecon version 1.4.3 Index]