read_raw {IrisSpatialFeatures} | R Documentation

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

### 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')

[Package IrisSpatialFeatures version 1.3.0 Index]