Proposed Analysis: Create manuscript tables

[jharenza]

What are the scientific goals of the analysis?

Create manuscript tables and supplemental tables - Table 1, S1, and S2 for now

What methods do you plan to use to accomplish the scientific goals?

• Create tables directory in main dir (https://github.com/AlexsLemonade/OpenPBTA-analysis) and put scripts and tables there.
• Either export TSV from this repo as EXCEL files or combine tables into multi-tab excel files and export as per listed below; name them with the appropriate table numbers

What input data are required for this analysis?

Table 1: Molecular subtypes determined for this project

• Create table using:

  subtypes <- v21 %>%
  filter(!is.na(pathology_diagnosis) & !is.na(molecular_subtype) & !grepl("To be classified", molecular_subtype))
  subtype_table <- subtypes %>%
  group_by(broad_histology, molecular_subtype) %>%
  tally() %>%
  write_tsv("subtypes-n.tsv")

Table S1: V21 histologies table

• convert v21 to excel

Table S2: DNA results table

• Create multi-tab file of:
  1. TMB (3 columns - BS_ID, TMB_coding from: tcga-snv-mutation-tmb-coding.tsv, and TMB_all from: tcga-snv-mutation-tmb-all.tsv)
  2. Mutational signatures - COSMIC (create matrix of BS_ID and signature weights similar to 4 below - from this table: https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/master/analyses/mutational-signatures/results/cosmic_signatures_results.tsv where signature weight is labeled mut_per_mb in the table)
  3. Mutational signatures - Alexandrov (create matrix of BS_ID and signature weights similar to 4 below - from this table: https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/master/analyses/mutational-signatures/results/nature_signatures_results.tsv where signature weight is labeled mut_per_mb in the table)
  4. Mutational signatures - CNS (mean matrix within https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/master/analyses/mutational-signatures/results/fitted_cns_signature_exposures.RDS)
  5. Chromothripsis regions per sample (https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/master/analyses/chromothripsis/results/chromothripsis_summary_per_sample.txt)

Table S3: RNA results table

• Create multi-tab file of:
  1. TP53 scores (https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/master/analyses/tp53_nf1_score/results/tp53_altered_status.tsv)
  2. EXTEND scores (BS_ID and normalized EXTEND scores from https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/master/analyses/telomerase-activity-prediction/results/TelomeraseScores_PTBAPolya_counts.txt and https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/master/analyses/telomerase-activity-prediction/results/TelomeraseScores_PTBAStranded_FPKM.txt)

How long do you expect is needed to complete the analysis? Will it be a multi-step analysis?

2-3 days

Who will complete the analysis (please add a GitHub handle here if relevant)?

@runjin326

What relevant scientific literature relates to this analysis?

NA

[jharenza]

closing with #1199