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

Description Usage Arguments Value Examples

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

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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

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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'))

IrisSpatialFeatures documentation built on May 2, 2018, 2:49 a.m.