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

Description Usage Arguments Value Examples

Description

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

Usage

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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

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

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