layers_example: Formatted layers object

In DrDimont: Drug Response Prediction from Differential Multi-Omics Networks

Formatted layers object

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:

groupA

Data associated with 'groupA'

data

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

identifiers

Data frame containing one column per ID

groupB

Data associated with 'groupB'

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, phosphosite and metabolite layers. The mRNA, protein and phosphosite data was adapted and reduced 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). The 'data' elements contain the raw data with samples as columns and molecular entities as rows. The 'identifiers' elements contain layer specific identifiers for the molecular entities, e.g, gene_name.

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

DrDimont documentation built on Sept. 23, 2022, 5:06 p.m.