lung_FDA {mxfda}

Multiplex imaging data from a non-small cell lung cancer study

Description

This data is adapted from the VectraPolarisData Bioconductor package. There are multiple ROIs for each patient.

Usage

lung_FDA

Format

lung_FDA

An mxFDA object with augmented non-small cel lung cancer multiplex immunofluorescence data, and NN G(r) calculated:

Metadata

information about the spatial samples with column sample_key column in both

Spatial

cell-level information with x and y columns along with sample_key to link to Metadata

subject_key

column in Metadata that may have multiple sample_key values for each, akin to patient IDs

sample_key

column in both Metadata and Spatial that is a 1:1 with the samples (unique per sample)

univariate_summaries

univariate summary slot with nearest neighbor G calculared

bivariate_summaries

empty slot available for bivariate summaries

functional_pca

empty slot for functional PCA data of summaries

functional_cox

empty slot for functional models

Details

Spatial summary functions of lung cancer multiplex imaging data.

This data is adapted from the VectraPolarisData Bioconductor package. Signal between the survival outcome and spatial summary functions has been augmented for teaching purposes. Spatial relationship is summarized using the nearest neighbor G function.

Includes only spatial samples that had 10 or more radii with calculable G function

Source

https://bioconductor.org/packages/release/data/experiment/html/VectraPolarisData.html