threshold_dataset {IrisSpatialFeatures} | R Documentation

## This function reads the manually determined thresholds of certain markers (e.g. PD1, PD-L1) and splits selected celltypes into marker+ and marker- celltypes.

### Description

This function reads the manually determined thresholds of certain markers (e.g. PD1, PD-L1) and splits selected celltypes into marker+ and marker- celltypes.

### Usage

    threshold_dataset(image_set, marker, marker_name, base = NULL,
      pheno_name = "Phenotype", remove_blanks = TRUE)

    ## S4 method for signature 'ImageSet'
    threshold_dataset(image_set, marker, marker_name,
      base = NULL, pheno_name = "Phenotype", remove_blanks = TRUE)

### Arguments

`image_set` | IrisSpatialFeatures ImageSet object.
`marker` | Name of the marker used in the score file.
`marker_name` | corresponding name, which should be appended at the selected cell types.
`base` | Vector of cell types for which the marker should be used.
`pheno_name` | Name of the phenotype column to be used. (Default from inForm is "Phenotype")
`remove_blanks` | Flag that indicates whether or not not called cells are to be removed. (Default: TRUE)

### Value

IrisSpatialFeatures ImageSet object.

### Examples

    dataset <- read_raw(path=system.file("extdata", package = "IrisSpatialFeatures"),
                         format='Mantra')
    dataset <- threshold_dataset(dataset,
                                 marker='PD-Ligand-1 (Opal 690)',
                                 marker_name='PDL1',
                                 base=c('SOX10+'))
    dataset <- threshold_dataset(dataset,
                                 marker='PD-1 (Opal 540)',
                                 marker_name='PD1',
                                 base=c('CD8+','OTHER'))

[Package IrisSpatialFeatures version 1.3.0 Index]