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Revamp

Fix gene boundaries

  • State “DONE” from “WAIT” [2019-08-07 Wed 15:25]
  • State “WAIT” from “TODO” [2019-08-07 Wed 15:25]

Re-run VEGAS (GENESIS, BCAC, conventional GWAS)

  • State “DONE” from “WAIT” [2019-08-18 Sun 16:56]
  • State “WAIT” from “TODO” [2019-08-07 Wed 11:37]

Check if the results match on X chromosome

  • State “DONE” from “WAIT” [2019-08-07 Wed 16:25]
  • State “WAIT” from “TODO” [2019-08-07 Wed 16:25]

Re-name gene method scripts to new *.nf convention

  • State “DONE” from “WAIT” [2019-08-07 Wed 15:33]
  • State “WAIT” from “TODO” [2019-08-07 Wed 15:33]

Progressively check if old results match & update manuscript accordingly

  • State “DONE” from “WAIT” [2019-08-12 Mon 18:05]
  • State “WAIT” from “TODO” [2019-08-12 Mon 18:05]

Re-run gene methods

  • State “DONE” from “WAIT” [2019-08-12 Mon 12:46]
  • State “WAIT” from “TODO” [2019-08-09 Fri 16:33]

Implement HotNet2 as in PEGASUS paper

  • State “DONE” from “WAIT” [2019-09-14 Sat 12:01]
  • State “WAIT” from “TODO” [2019-09-12 Thu 19:40]

Do-nothing in Lasso

  • State “DONE” from “WAIT” [2019-08-13 Tue 16:40]
  • State “WAIT” from “TODO” [2019-08-12 Mon 16:14]

Work on the manuscript

  • State “DONE” from “WAIT” [2019-08-13 Tue 18:15]
  • State “WAIT” from “TODO” [2019-08-13 Tue 18:15]

Computational time benchmark

  • State “DONE” from “WAIT” [2019-08-14 Wed 16:25]
  • State “WAIT” from “TODO” [2019-08-14 Wed 16:25]

HT vs LC+HT comparison

  • State “DONE” from “WAIT” [2019-09-09 Mon 14:37]
  • State “WAIT” from “TODO” [2019-09-09 Mon 14:37]

Try L2 penalty

  • State “DONE” from “WAIT” [2019-08-15 Thu 17:56]
  • State “WAIT” from “TODO” [2019-08-15 Thu 17:56]

Runtime benchmark

  • State “DONE” from “WAIT” [2019-09-14 Sat 12:01]

WAIT Runtime LC benchmark

Read network papers

Use LEAN P-value? Write authors?

Use LEAN P-value? Write authors?

  • State “DONE” from “WAIT” [2019-09-09 Mon 14:35]
  • State “WAIT” from “TODO” [2019-09-09 Mon 14:35]

Checked the vignette:https://cran.r-project.org/web/packages/LEANR/vignettes/CCM-data.html

Run SigMod on SNP network

Figure 4D: points, log scale?

  • State “DONE” from “WAIT” [2019-09-05 Thu 15:55]
  • State “WAIT” from “TODO” [2019-09-05 Thu 15:55]

Remove nodes selected only by one methods

  • State “DONE” from “WAIT” [2019-09-05 Thu 16:00]
  • State “WAIT” from “TODO” [2019-09-05 Thu 16:00]

Supp figure with consensus with all genes names

  • State “DONE” from “WAIT” [2019-09-09 Mon 14:38]
  • State “WAIT” from “TODO” [2019-09-09 Mon 14:38]

Replace Jaccard index by Pearson correlation

  • State “DONE” from “WAIT” [2019-09-10 Tue 16:36]
  • State “WAIT” from “TODO” [2019-09-10 Tue 16:36]

Replace Lasso by “Comparative performances of machine learning methods for classifying Crohn Disease patients using genome-wide genotyping data”

Parametrize max % of SNPs

Add baseline for sensitivity and specificity based on dataset imbalance

  • State “DONE” from “WAIT” [2019-09-19 Thu 09:01]
  • State “WAIT” from “TODO” [2019-09-19 Thu 09:01]

Standardize HotNet2 output

  • State “DONE” from “WAIT” [2019-09-19 Thu 08:01]
  • State “WAIT” from “TODO” [2019-09-19 Thu 08:01]

WAIT Run benchmark with HotNet2

  • State “WAIT” from “TODO” [2019-09-19 Thu 08:01]

Manuscript

Introduction

  • State “DONE” from “WAIT” [2019-08-09 Fri 16:34]
  • State “WAIT” from “TODO” [2019-08-09 Fri 16:34]

Update all analyses with new SConES

  • State “DONE” from “WAIT” [2019-09-09 Mon 14:38]
  • State “WAIT” from “TODO” [2019-09-09 Mon 14:38]

Discussion on biology of familial BRCA

  • State “DONE” from “WAIT” [2019-09-09 Mon 14:38]
  • State “WAIT” from “TODO” [2019-09-09 Mon 14:38]

OncoDrive paper

Run LMM

See possible directions

Check if VEGAS without covariate correction has significant genes

OncoDRIVE

Check license date

Use SNP networks for everything

Check p-value shift

Describe state of the art: comparison between methods

Run benchmark

  • State “DONE” from “WAIT” [2019-08-01 Thu 02:04]
  • State “WAIT” from “DONE” [2019-07-28 Sun 17:02]
  • State “DONE” from “WAIT” [2019-07-26 Fri 09:56]
  • State “WAIT” from “TODO” [2019-07-19 Fri 14:58]

Add Jaccard indexes to compute stability

  • State “DONE” from “WAIT” [2019-07-19 Fri 16:14]
  • State “WAIT” from “TODO” [2019-07-19 Fri 16:14]

Test Jaccard indexes

  • State “DONE” from “WAIT” [2019-07-25 Thu 14:36]
  • State “WAIT” from “TODO” [2019-07-25 Thu 14:22]

Run Lasso on a node

  • State “DONE” from “WAIT” [2019-08-01 Thu 02:56]
  • State “WAIT” from “TODO” [2019-08-01 Thu 02:54]

It will require bigmem.

Run methods

Check SConES solution/use old algorithm

Handle dmGWAS solutions in benchmark

Add HotNet2

Pathway enrichment analysis on consensus

CANCELED Re-run SConES with new genes

  • State “CANCELED” from “DONE” [2019-07-25 Thu 16:38]
    It was done.
  • State “DONE” from “WAIT” [2019-07-25 Thu 16:38]
  • State “WAIT” from “TODO” [2019-07-25 Thu 16:38]

Run HotNet2

  • State “DONE” from “WAIT” [2019-08-14 Wed 15:45]
  • State “WAIT” from “TODO” [2019-07-25 Thu 18:05]

Verify that the conclusions from old notebooks hold

  • State “DONE” from “WAIT” [2019-08-06 Tue 18:47]
  • State “WAIT” from “TODO” [2019-08-06 Tue 18:47]

Check for how many genes VEGAS is mistaken

  • State “DONE” from “WAIT” [2019-08-07 Wed 11:25]
  • State “WAIT” from “TODO” [2019-08-07 Wed 11:25]

Act accordingly.

Check room for 3rd year thesis committee

Submit application to Training Unit

Prepare OncoDRIVE paper after GENESIS as Letter.

Figure out how to correct by population structure

  • State “DONE” from “WAIT” [2019-07-25 Thu 17:05]
  • State “WAIT” from “TODO” [2019-07-25 Thu 17:05]

Correct by population structure as in Association analysis identifies 65 new breast cancer risk loci

  • State “DONE” from “WAIT” [2019-08-01 Thu 04:21]
  • State “WAIT” from “TODO” [2019-07-25 Thu 22:45]

“To adjust for potential (intra-continental) popu- lation stratification in the OncoArray dataset, principal components analysis was performed using data from 33,661 uncorrelated SNPs (which included 2,318 SNPs specifically selected on informativeness for determining continental ancestry) with a MAF of at least 0.05 and maximum correlation of 0.1 in the OncoArray dataset, using purpose-written software (http://ccge.medschl.cam.ac.uk/software/pccalc). For the main analyses, we used the first ten principal components, as additional components did not further reduce inflation in the test statistics. We used nine principal components for the iCOGS and up to ten principal components for the other GWAS, where this was found to reduce inflation.”

CANCELED Check population structure on PCs

  • State “CANCELED” from “DONE” [2019-08-07 Wed 11:43]
    New approach will be used
  • State “DONE” from “WAIT” [2019-08-07 Wed 11:43]
  • State “WAIT” from “TODO” [2019-08-07 Wed 11:43]

Find out genomic inflation by # of PC. Find out the number of PCs to use. As we have less samples than the original study, maybe not 10 PCs are needed.

Finish details on GENESIS: dataset and preprocessing

Preparation for the e-mail and for the paper.

Write e-mail to Nadine and Fabienne

ISMB

Book ISMB

Ordre de Service

Add acknowledgements

Re-read Block HSIC Lasso paper

  • State “DONE” from “WAIT” [2019-07-24 Wed 14:11]
  • State “WAIT” from “TODO” [2019-07-24 Wed 14:11]

Check Block HSIC Lasso runtime and memory consumption

  • State “DONE” from “WAIT” [2019-07-24 Wed 14:11]
  • State “WAIT” from “TODO” [2019-07-24 Wed 14:11]

CANCELED Write summary for RIKEN talk

  • State “CANCELED” from “DONE” [2019-07-25 Thu 12:21]
    Makoto did it.
  • State “DONE” from “WAIT” [2019-07-25 Thu 12:21]
  • State “WAIT” from “TODO” [2019-07-25 Thu 12:21]

Run Vegas with top 5, 15 and 20%

  • State “DONE” from “WAIT” [2019-08-07 Wed 11:32]
  • State “WAIT” from “TODO” [2019-08-07 Wed 11:32]
  • State “WAIT” from “DONE” [2019-08-07 Wed 11:31]

Alternative to VEGAS

Implement SKAT

  • State “DONE” from “WAIT” [2019-08-06 Tue 19:14]
  • State “WAIT” from “TODO” [2019-08-06 Tue 19:14]

CANCELED Check others

  • State “CANCELED” from “DONE” [2019-08-06 Tue 19:14]
    Just try to fix vegas
  • State “DONE” from “WAIT” [2019-08-06 Tue 19:14]
  • State “WAIT” from “TODO” [2019-08-06 Tue 19:14]

BCAC comparison

Compare gene results to BCAC

Check if SNPs are imputed

BCAC mixes OncoArray and iCOGS. Hence, it will need imputation. Be careful that they do not introduce artifacts.

Compare SNP results to BCAC

Compute BCAC gene-level results

Run VEGAS only on iCOGS SNPs

Re-run BCAC Jupyter analysis

  • State “DONE” from “WAIT” [2019-08-19 Mon 12:26]
  • State “WAIT” from “TODO” [2019-08-19 Mon 12:26]

Manuscript

Prepare method-wise list of biomarkers

  • State “DONE” from “WAIT” [2019-08-12 Mon 14:27]
  • State “WAIT” from “TODO” [2019-08-12 Mon 14:27]

LEAN

dmGWAS

SigMod

CANCELED Finish introduction

  • State “CANCELED” from “DONE” [2019-08-07 Wed 11:42]
    New task created not to feel terrible about it
  • State “DONE” from “WAIT” [2019-08-07 Wed 11:42]
  • State “WAIT” from “TODO” [2019-08-07 Wed 11:42]

Finish SNP and gene-level results

Fix SConES and dmGWAS

CANCELED Figure out how to select modules in Hierarchical Hotnet

  • State “CANCELED” from “DONE” [2019-07-19 Fri 14:56]
    Hierarchical HotNet ditched for HotNet2.
  • State “DONE” from “WAIT” [2019-07-19 Fri 14:56]
  • State “WAIT” from “TODO” [2019-07-19 Fri 14:56]

Convert SConES GM to gene network to build consensus

Plot SConES GS and GM results

Add known BRCA genes to consensus network

SNP BCAC comparison

  • State “DONE” from “WAIT” [2019-08-27 Tue 19:54]
  • State “WAIT” from “TODO” [2019-08-27 Tue 19:54]

Add software references

Fix several TODOs in the manuscript

Print manuscript for Chloe

Move Chloe’s comments into the manuscript

CANCELED Update outdated parts of the manuscript

  • State “CANCELED” from “DONE” [2019-08-07 Wed 11:45]
    new revamp
  • State “DONE” from “WAIT” [2019-08-07 Wed 11:45]
  • State “WAIT” from “TODO” [2019-08-07 Wed 11:45]

HT vs LC networks

Prepare HINT LC

Think about the problem

Implement solution approved by Chloe

  • State “DONE” from “WAIT” [2019-07-19 Fri 16:22]
  • State “WAIT” from “TODO” [2019-07-19 Fri 16:22]

Run benchmark HT+LC

  • State “DONE” from “WAIT” [2019-08-04 Sun 16:28]
  • State “WAIT” from “TODO” [2019-07-25 Thu 16:15]

Analyse HT+LC

  • State “DONE” from “WAIT” [2019-08-04 Sun 16:29]
  • State “WAIT” from “TODO” [2019-08-04 Sun 16:29]

Genes not in the network

Finish analysis

Re-run SigMod with old PPI + old scores? Check FGFR2.

  • State “DONE” from “WAIT” [2019-08-01 Thu 02:56]
  • State “WAIT” from “TODO” [2019-07-25 Thu 16:31]

Finish HotNet2 implementation

  • State “DONE” from “WAIT” [2019-07-22 Mon 15:27]
  • State “WAIT” from “TODO” [2019-07-22 Mon 15:27]