layers_example: Formatted layers object

In molnet-org/molnet: Predicting Differential Drug Response using Multi-Omics Networks

Description

Exemplary intermediate pipeline output containing a correctly formatted layers list.

Usage

layers_example

Format

A list with 4 items. Each layer list contains 2 groups and a 'name' element. Each group contains 'data' and 'identifiers'. The structure for one individual layer:

group1

Data associated with group1

data

Raw data. Components (e.g. genes) in columns, samples in rows

identifiers

Data frame containing one column per ID

group2

Data associated with group2

data

see above

identifiers

see above

name

Name of the layer

Details

List containing four layer items created by make_layer. Each layer contains 'data' and 'identifiers' stratified by group and a 'name' element giving the layer name. The data contained in this example refers to mRNA, protein, phosphoprotein and metabolite layers. The data on mRNA, protein and phosphoproteins in taken from Krug et al., 2020 containing data from the Clinical Proteomic Tumor Analysis Consortium (CPTAC). The metabolite data was sampled randomly to generate distributions similar to those reported (e.g., in Terunuma et al., 2014).

Source

Terunuma, Atsushi et al. “MYC-driven accumulation of 2-hydroxyglutarate is associated with breast cancer prognosis.” The Journal of clinical investigation vol. 124,1 (2014): 398-412. doi:10.1172/JCI71180

Krug, Karsten et al. “Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy.” Cell vol. 183,5 (2020): 1436-1456.e31. doi:10.1016/j.cell.2020.10.036

molnet-org/molnet documentation built on Dec. 21, 2021, 8:59 p.m.