Add dataset and repeat co-mut plot and gene pairs analysis

zhoulab / sclc-scripts

scripts for "Significantly mutated genes and regulatory pathways in SCLC—a meta-analysis"

https://doi.org/10.1016/j.cancergen.2017.05.003

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Add dataset and repeat co-mut plot and gene pairs analysis #3

Closed varsh1090 closed 7 years ago

varsh1090 commented 7 years ago

To add a new dataset with 44 samples to the previous analyses.

varsh1090 commented 7 years ago

Updated file in - ZhouLab Team Folder/People/BioinfoUndergrads/SCLCproject/4dataset_nonsilent

varsh1090 commented 7 years ago

Updated input files uploaded to sclc-scripts/data/ in github as well.

victorlin commented 7 years ago

Some errors that can't be handled by the current script:

Lines 2340, 3216, 5861, and 6734 in 4dataset_nonsilent.txt are empty.
The p-value (and q-value) for TP53 in SigGenes_001_010317.txt has value 0.

varsh1090 commented 7 years ago

Data for gene pairs analysis - Dropbox (ZhouLab)/ZhouLab Team Folder/Projects/Oncogenomics/SCLC/Mutsig/HeuristicAnalysis/GenePairs/4datasets_genepairs

varsh1090 commented 7 years ago

New source files -

genenonsilent200.txt to be replaced with 4dataset_nonsilent.txt
PercDict.dic and GeneNumDict.dic can be generated from file - 4datasets_GenePerc.txt (Column 1 is gene, column 2 is GeneNum and column 3 is GenePerc)
Gene list to be used - 4datasets_MoreThan2

varsh1090 commented 7 years ago

Repeat analysis for gene lists - SigGenes_001_list.txt and SigGenes_005_list.txt