as.Seurat: Convert GeoMxSet Object to SeuratObject

In Nanostring-Biostats/GeomxTools: NanoString GeoMx Tools

Convert GeoMxSet Object to SeuratObject

Description

Convert GeoMxSet Object to SeuratObject

Usage

## S3 method for class 'NanoStringGeoMxSet'
as.Seurat(
  x,
  ident = NULL,
  normData = NULL,
  coordinates = NULL,
  forceRaw = FALSE,
  ...
)

Arguments

x	An object to convert to class Seurat
ident	column in GeoMxSet segmentProperties to set as Seurat object's identity class
normData	assay containing normalized data
coordinates	X and Y coordinates of each ROI, format: c(X,Y)
forceRaw	should raw data be forced into SeuratObject, not recommended
...	Arguments passed to other methods

Value

SeuratObject containing GeoMx data

See Also

SeuratObject::as.Seurat

Examples

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

target_demoData <- aggregateCounts(demoData[1:1000,1:10])

target_demoData <- normalize(target_demoData, "quant")

seurat_demoData <- as.Seurat(target_demoData, ident = "cell_line",
                             normData = "exprs_norm", forceRaw = FALSE)

Nanostring-Biostats/GeomxTools documentation built on Sept. 24, 2024, 4:51 p.m.