Create Seurat object

Source: R/createSeuratObj.R

Create Seurat object from output of ExportCellDetectionMeasurement.groovy

createSeuratObj(
  path,
  useValue = c("Mean", "Median", "Min", "Max", "Std.Dev"),
  markerLocations = "Cell",
  ...
)

Arguments

path

character(1L) or connection. The path to measurements exported by ExportCellDetectionMeasurement.groovy in QuPath.

useValue

character(1L). The values should be used as count table.

markerLocations

The marker locations for each marker or charcter(1L) for all markers. The possible locations are 'Nucleus', and 'Cell'. 'Cytoplasm' and 'Membrane' are also available but not suggested.

...

parameters could be used by CreateSeuratObject

Value

An Seurat object.

Examples

# example code
tsv <- system.file("extdata", "test.qptiff.tsv.zip",
                   package = "cdQuPath",
                   mustWork = TRUE)
seu <- createSeuratObj(tsv, useValue = 'Median',
                       markerLocations = CodexPredefined$markerLocations)
#> Warning: Layer counts isn't present in the assay object; returning NULL
#> Warning: Layer counts isn't present in the assay object; returning NULL
#> Warning: Layer counts isn't present in the assay object; returning NULL
#> Warning: Layer counts isn't present in the assay object; returning NULL
#> Warning: Layer counts isn't present in the assay object; returning NULL
#> Warning: Layer counts isn't present in the assay object; returning NULL
#> Warning: Layer counts isn't present in the assay object; returning NULL
#> Warning: Layer counts isn't present in the assay object; returning NULL
#> Warning: Layer counts isn't present in the assay object; returning NULL
#> Warning: Layer counts isn't present in the assay object; returning NULL
#> Warning: Layer counts isn't present in the assay object; returning NULL
#> Warning: Layer counts isn't present in the assay object; returning NULL
#> Warning: Layer counts isn't present in the assay object; returning NULL
#> Warning: Layer counts isn't present in the assay object; returning NULL
#> Warning: Layer counts isn't present in the assay object; returning NULL
#> Warning: Layer counts isn't present in the assay object; returning NULL
#> Warning: Layer counts isn't present in the assay object; returning NULL
#> Warning: Layer counts isn't present in the assay object; returning NULL
#> Warning: Layer counts isn't present in the assay object; returning NULL
#> Warning: Layer counts isn't present in the assay object; returning NULL
#> Warning: Layer counts isn't present in the assay object; returning NULL
#> Warning: Layer counts isn't present in the assay object; returning NULL
#> Warning: Layer counts isn't present in the assay object; returning NULL
#> Warning: Layer counts isn't present in the assay object; returning NULL
seu
#> An object of class Seurat 
#> 600 features across 102 samples within 25 assays 
#> Active assay: RNA (24 features, 0 variable features)
#>  1 layer present: counts
#>  24 other assays present: Nucleus_Mean, Nucleus_Median, Nucleus_Min, Nucleus_Max, Nucleus_Std.Dev., Nucleus_Variance, Cytoplasm_Mean, Cytoplasm_Median, Cytoplasm_Min, Cytoplasm_Max, Cytoplasm_Std.Dev., Cytoplasm_Variance, Membrane_Mean, Membrane_Median, Membrane_Min, Membrane_Max, Membrane_Std.Dev., Membrane_Variance, Cell_Mean, Cell_Median, Cell_Min, Cell_Max, Cell_Std.Dev., Cell_Variance
#>  1 dimensional reduction calculated: pos