Notes on the RNAsum Rmd structure for developers
ref_dataset.list
Processed data with following elements:
| Element | Description |
|---|---|
[[dataset]][["combined_data"]] |
combined read count data (ref + sample datasets)
(combineDatasets output in chunk
load_ref_data) |
[[dataset]][["sample_annot"]] |
combined data samples annotation (“combineDatasets()” output in chunk “load_ref_data”) |
[[dataset]][["clinical_info"]] |
clinical (survival + treatment) info |
[[dataset]][["combined_data_processed"]] |
transformed, filtered and normalised data (chunks “data_transformation” and “data_normalisation”) |
[[dataset]][["batch_effect_corrected"]] |
transformed, filtered, normalised and batch effect corrected data (chunk “batch_effect_correction”) |
[[dataset]][["pca_combined_data_processed"]] |
PCA results for combined data |
[[dataset]][["pca_batch_effect_corrected"]] |
PCA results for batch-effect corrected data |
[[dataset]][["rle_combined_data_processed"]] |
RLE plot for combined data |
[[dataset]][["rle_batch_effect_corrected"]] |
RLE plot for batch-effect corrected data |
[[dataset]][["data_to_report"]] |
fully combined and processed data for reporting |
[[dataset]][["gene_annot_all"]] |
gene annotation for combined read count data, containing all input genes. Includes SYMBOL, GENEBIOTYPE, ENSEMBL, SEQNAME, GENESEQSTART, and GENESEQEND. ENSEMBL is used for rownames. |
[[dataset]][["gene_annot"]] |
gene annotation for transformed, filtered and normalised data. Includes SYMBOL, GENEBIOTYPE, ENSEMBL, SEQNAME, GENESEQSTART, GENESEQEND. SYMBOL is used for rownames. |
[[dataset]][["expr_mut_cn_data_all"]] |
combined expression, mutation and CN data. |
[[dataset]][["expr_mut_cn_data"]] |
combined expression, mutation and CN data limited to cancer genes that meet user-defined CN values threshold. |
ref_genes.list
Genes of interest with following gene sets:
| Element | Description |
|---|---|
[["genes_cancer"]] |
list of cancer genes derived from UMCCR Cancer Gene list (https://github.com/vladsaveliev/NGS_Utils/blob/master/ngs_utils/reference_data/key_genes/umccr_cancer_genes.2019-03-20.tsv) and OncoKB portal (http://oncokb.org/#/cancerGenes) |
[["genes_oncokb"]] |
list of cancer genes derived from OncoKB only (although genes present in the UMCCR panel are also flagged) |
[["genes_immune"]] |
list of immune reponse markers provided in the “An Immunogram for the Cancer-Immunity Cycle” paper by Karasaki at al (2017) (https://www.ncbi.nlm.nih.gov/pubmed/28088513) and OmniSeq report (https://www.omniseq.com/) |
[["genes_hrd"]] |
list of hrd genes |
[["pcgr"]] |
list and PCGR annotation of indels |
[["purple"]] |
list and PURPLE annotation of CN altered genes |
[["manta"]] |
list and Manta annotation of SVs |
[["arriba"]] |
list and Arriba annotation of gene fusion events |
[["pizzly"]] |
list and Pizzly annotation of gene fusion events |
[["summary"]] |
summary of above-mentioned gene lists, also used for expression summary tables and plots. |