read_raw: Read inForm output and store it in an IrisSpatialFeatures...

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

Description

Read inForm output and store it in an IrisSpatialFeatures ImageSet object.

Usage

read_raw(path, label_fix = list(), format = "Vectra", dir_filter = "",
  read_nuc_seg_map = FALSE, MicronsPerPixel = 0.496,
  invasive_margin_in_px = 100, readMasks = TRUE, ignore_scoring = FALSE,
  read_only_relevant_markers = TRUE)

## S4 method for signature 'character'
read_raw(path, label_fix = list(), format = "Vectra",
  dir_filter = "", read_nuc_seg_map = FALSE, MicronsPerPixel = 0.496,
  invasive_margin_in_px = 100, readMasks = TRUE, ignore_scoring = FALSE,
  read_only_relevant_markers = TRUE)

Arguments

path	Directory that contains the raw files
label_fix	List of length 2 character vector that is used to fix filenames.
format	Output format: Currently only "Vectra" and "Mantra" are supported.
dir_filter	Filter to select only certain directory names.
read_nuc_seg_map	Flag indicating whether the nuclear map should be read.
MicronsPerPixel	Length of one pixel. Default: 0.496, corresponding to a 20x Mantra/Vectra images
invasive_margin_in_px	The width of the invasive margin in pixels
readMasks	Flag indicating whether the "_Tumor.tif" and "_Invasive_Margin.tif" should be read (default: True)
ignore_scoring	Flag indicating whether the scoring file should be ignored (default: False)
read_only_relevant_markers	Flag that indicates whether all read inform output should be kept or only the relevant markers

Value

IrisSpatialFeatures ImageSet object.

Examples

 raw_data <- read_raw(path=system.file("extdata", package = "IrisSpatialFeatures"),
                      format='Mantra')

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