Updated analysis: Annotate SNV table of gene-level mutation frequencies

[logstar]

What analysis module should be updated and why?

The snv-frequencies module needs to be updated to generate gene-level SNV frequency tables.

What changes need to be made? Please provide enough detail for another participant to make the update.

Generate gene-level SNV frequency tables.

Add a column for gene_type and annotate kinase, TF, oncogene, TSG per this file. The sources of this file is described at https://github.com/d3b-center/annoFuse#prerequisites-for-cohort-level-analysis.

• Updated analysis: add pedcbio links to SNV tables #83 When this issue is completed, add kf-pecbio oncoprint and lollipop plot URLs as additional columns.

What input data should be used? Which data were used in the version being updated?

snv-consensus-plus-hotspots.maf.tsv.gz

When do you expect the revised analysis will be completed?

1-2 days.

Who will complete the updated analysis?

@logstar

cc: @jharenza

[logstar]

@jharenza Regarding the gene_types in the genelistreference.txt, I wonder if I should add a column for each type and use Y/N as values, in order to handle gene symbols that are mapped to more than one types, like the following ones:

> gsb_gtype_df <- read_tsv('../fusion_filtering/references/genelistreference.txt',
+                          col_types = cols(.default = col_guess()))
> gsb_gtype_df %>%
+   group_by(Gene_Symbol) %>%
+   summarise(n_uniq_types = length(unique(type)),
+             types = paste(sort(unique(type)), collapse = ',')) %>%
+   filter(n_uniq_types > 1)
# A tibble: 1,166 x 3
   Gene_Symbol n_uniq_types types                       
   <chr>              <int> <chr>                       
 1 ABI1                   2 CosmicCensus,Oncogene       
 2 ABL1                   3 CosmicCensus,Kinase,Oncogene
 3 ABL2                   3 CosmicCensus,Kinase,Oncogene
 4 ACKR3                  2 CosmicCensus,Oncogene       
 5 ACSL3                  2 CosmicCensus,Oncogene       
 6 ACSL6                  2 CosmicCensus,Oncogene       
 7 ACVR1                  2 CosmicCensus,Kinase         
 8 ACVR1B                 2 Kinase,Oncogene             
 9 ACVR1C                 2 Kinase,TumorSuppressorGene  
10 ACVR2A                 3 CosmicCensus,Kinase,Oncogene
# … with 1,156 more rows

If a single gene_type column is preferred, could I use a comma separated list of unique types as values for the genes that have more than one types?

[logstar]

@jharenza I will proceed with adding a single Gene_type column to the gene-level SNV frequency table. If adding multiple Y/N columns is preferred, I will revise accordingly.

[logstar]

Closed with d3b-center/OpenPedCan-analysis#45 merged.