read_raw {IrisSpatialFeatures} | R Documentation |
Read inForm output and store it in an IrisSpatialFeatures ImageSet object.
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)
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 |
IrisSpatialFeatures ImageSet object.
raw_data <- read_raw(path=system.file("extdata", package = "IrisSpatialFeatures"), format='Mantra')