| layers_example {DrDimont} | R Documentation |
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