SpatialPosition-class: Class to Contain NanoString Spatial Overlay ROI information

In Nanostring-Biostats/SpatialOmicsOverlay: Spatial Overlay for Omic Data from Nanostring GeoMx Data

Class to Contain NanoString Spatial Overlay ROI information

Description

The SpatialPosition class organizes the pertinant ROI specific information from the OME-TIFFs

Usage

  SpatialPosition(position)

Arguments

position

data.frame containing information from the OME-TIFF: "ROILabel" order of ROIs "Sample_ID" unique identifier "Height" total height of ROI "Width" total width of ROI "X" top left corner (x coordinate) of ROI in total scan "Y" top left corner (y coordinate) of ROI in total scan "Segmentation" part of segmented ROI "Position" base64 encoding of coordinates

Value

An S4 class containing image data from a NanoString GeoMx experiment

Accessing

SpatialPosition objects have the following accessor methods:

spatialPos(object)

returns SpatialPosition object

meta(object)

extracts the metadata for each ROI, does not include the base64 encoding.

position(object)

extracts the base64 encoding for each ROI, CAUTION: very long strings.

See Also

SpatialOverlay-class

Nanostring-Biostats/SpatialOmicsOverlay documentation built on April 20, 2024, 5:36 a.m.