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

In gusef/Iris: 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 = "", dir_filter = "",
  read_nuc_seg_map = FALSE, MicronsPerPixel = 0.496,
  invasive_margin_in_px = 100, readTumorAndMarginMasks = FALSE,
  customMask = "", ignore_scoring = FALSE,
  read_only_relevant_markers = TRUE, specified_phenotypes = NULL,
  verbose = TRUE)

## S4 method for signature 'character'
read_raw(path, label_fix = list(), format = "",
  dir_filter = "", read_nuc_seg_map = FALSE, MicronsPerPixel = 0.496,
  invasive_margin_in_px = 100, readTumorAndMarginMasks = FALSE,
  customMask = "", ignore_scoring = FALSE,
  read_only_relevant_markers = TRUE, specified_phenotypes = NULL,
  verbose = 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. Autodetect by default.
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
readTumorAndMarginMasks	Flag indicating whether the "_Tumor.tif" and "_Invasive_Margin.tif" should be read (default: False)
customMask	Setting this indicates to the tif file for each frame with *_<customMask>.tif should be used as the mask. This overrides binary_seg mask.
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
specified_phenotypes	You can explicitly list which phenotypes are expected to be in the sample. This is useful when some values should be counted as zero when they are completely absent.
verbose	Print helpful information (default: True)

Value

IrisSpatialFeatures ImageSet object.

Examples

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

gusef/Iris documentation built on May 14, 2019, 2:42 p.m.