threshold_dataset: This function reads the manually determined thresholds of...

In gusef/IrisSpatialFeatures: A package to extract spatial features based on multiplex IF images

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'))

gusef/IrisSpatialFeatures documentation built on May 6, 2019, 9:50 p.m.