Rerun analyses

[komalsrathi]

This PR reruns all analyses with v1 release.

Fixes https://github.com/d3b-center/hope-cohort-analysis/issues/77, https://github.com/d3b-center/hope-cohort-analysis/issues/52

[jharenza]

hi @komalsrathi can you merge main/master into this? I think you are missing files in your survival module for eg

[komalsrathi]

I did that but might have done something weird if you are not seeing those files. I don't know if I deleted them by mistake.

(base) ➜  d3b-hope-cohort-analysis git:(rerun-analyses) git checkout master
Switched to branch 'master'

(base) ➜  d3b-hope-cohort-analysis git:(master) ✗ git pull origin master
From github.com:d3b-center/d3b-hope-cohort-analysis
 * branch            master     -> FETCH_HEAD
Already up to date.

(base) ➜  d3b-hope-cohort-analysis git:(master) ✗ git checkout rerun-analyses
Switched to branch 'rerun-analyses'

(base) ➜  d3b-hope-cohort-analysis git:(rerun-analyses) git merge origin/master
Already up to date.

[komalsrathi]

I'll check what is missing and add those files back from master.

[komalsrathi]

Could you tell me which files are missing?

branch master has 4 directories and 43 files:

(base) ➜  d3b-hope-cohort-analysis git:(master) ✗ tree analyses/survival-analysis
analyses/survival-analysis
├── 01-survival-analysis.R
├── 02-summary-statics-TP53.Rmd
├── 02-summary-statics-TP53.html
├── 03-survival-tp53.Rmd
├── 03-survival-tp53.html
├── README.md
├── input
│   ├── GBM_survial_tp53.tsv
│   └── HGG_survial_tp53.tsv
├── plots
│   ├── HR_DMG.pdf
│   ├── HR_DMG_tp53_interaction.pdf
│   ├── HR_HGG_WT.pdf
│   ├── HR_broad_mol_subtype.pdf
│   ├── HR_mol_subtype_without_tp53.pdf
│   ├── HR_molecular_subtype.pdf
│   ├── HR_race.pdf
│   ├── KM_binned_age.pdf
│   ├── KM_binned_tp53.pdf
│   ├── KM_broad_mol.pdf
│   ├── KM_mol_subtype_without_tp53.pdf
│   ├── KM_race.pdf
│   ├── KM_reported_gender.pdf
│   ├── boxplot_tp53_score_binned_age_2gp_aya.pdf
│   ├── boxplot_tp53_score_binned_age_3gp_aya.pdf
│   ├── boxplot_tp53_score_gender.pdf
│   ├── boxplot_tp53_score_race.pdf
│   ├── boxplot_tp53_score_status.pdf
│   └── boxplot_tp53_score_subtype.pdf
├── results
│   ├── DMG_score+reported_gender+molecular_subtype*tp53+binned_age.RDS
│   ├── DMG_score+reported_gender+molecular_subtype+binned_age.RDS
│   ├── HGG_H3WT_score+reported_gender+molecular_subtype+binned_age.RDS
│   ├── alt_status_vs_survival_multivariate.pdf
│   ├── alt_vs_survival_km.pdf
│   ├── msi_paired_vs_survival_multivariate.pdf
│   ├── msi_status_vs_survival_km.pdf
│   ├── msi_status_vs_survival_multivariate.pdf
│   ├── t_n_telomere_content_vs_survival_multivariate.pdf
│   ├── tp53_score+reported_gender+broad_mol+binned_age.RDS
│   ├── tp53_score+reported_gender+mol_subtype+binned_age.RDS
│   ├── tp53_score+reported_gender+mol_subtype_without_tp53+binned_age.RDS
│   └── tp53_score+reported_gender+race+binned_age.RDS
└── utils
    ├── plotForest.R
    ├── survival_models.R
    └── theme_for_plot.R

4 directories, 43 files

branch rerun-analyses has 4 directories and 43 files:

(base) ➜  d3b-hope-cohort-analysis git:(rerun-analyses) tree analyses/survival-analysis
analyses/survival-analysis
├── 01-survival-analysis.R
├── 02-summary-statics-TP53.Rmd
├── 02-summary-statics-TP53.html
├── 03-survival-tp53.Rmd
├── 03-survival-tp53.html
├── README.md
├── input
│   ├── GBM_survial_tp53.tsv
│   └── HGG_survial_tp53.tsv
├── plots
│   ├── HR_DMG.pdf
│   ├── HR_DMG_tp53_interaction.pdf
│   ├── HR_HGG_WT.pdf
│   ├── HR_broad_mol_subtype.pdf
│   ├── HR_mol_subtype_without_tp53.pdf
│   ├── HR_molecular_subtype.pdf
│   ├── HR_race.pdf
│   ├── KM_binned_age.pdf
│   ├── KM_binned_tp53.pdf
│   ├── KM_broad_mol.pdf
│   ├── KM_mol_subtype_without_tp53.pdf
│   ├── KM_race.pdf
│   ├── KM_reported_gender.pdf
│   ├── boxplot_tp53_score_binned_age_2gp_aya.pdf
│   ├── boxplot_tp53_score_binned_age_3gp_aya.pdf
│   ├── boxplot_tp53_score_gender.pdf
│   ├── boxplot_tp53_score_race.pdf
│   ├── boxplot_tp53_score_status.pdf
│   └── boxplot_tp53_score_subtype.pdf
├── results
│   ├── DMG_score+reported_gender+molecular_subtype*tp53+binned_age.RDS
│   ├── DMG_score+reported_gender+molecular_subtype+binned_age.RDS
│   ├── HGG_H3WT_score+reported_gender+molecular_subtype+binned_age.RDS
│   ├── alt_status_vs_survival_multivariate.pdf
│   ├── alt_vs_survival_km.pdf
│   ├── msi_paired_vs_survival_multivariate.pdf
│   ├── msi_status_vs_survival_km.pdf
│   ├── msi_status_vs_survival_multivariate.pdf
│   ├── t_n_telomere_content_vs_survival_multivariate.pdf
│   ├── tp53_score+reported_gender+broad_mol+binned_age.RDS
│   ├── tp53_score+reported_gender+mol_subtype+binned_age.RDS
│   ├── tp53_score+reported_gender+mol_subtype_without_tp53+binned_age.RDS
│   └── tp53_score+reported_gender+race+binned_age.RDS
└── utils
    ├── plotForest.R
    ├── survival_models.R
    └── theme_for_plot.R

4 directories, 43 files

[jharenza]

I see them now, I am not sure what happened- looks like they were updated around 4 pm!

[komalsrathi]

Code works fine! I leave a few comments. Besides the comments in scripts, do we also need to update the bash script [run_full_analysis.sh](https://github.com/d3b-center/hope-cohort-analysis/blob/master/run_full_analysis.sh)?

I removed this script as it isn't needed anymore.

[jharenza]

@komalsrathi v2 is live

[komalsrathi]

I have updated all modules with v2 except for oncoplots which I will do tomorrow after discussing on the call.

[komalsrathi]

Hi! I think this PR is ready for review with the most up to date changes asked by @mkoptyra. Any chance of getting this reviewed and merged this week? If not then no worries. Thank you!

[komalsrathi]

Any ETA on this PR? I would like to get this merged if possible - not sure what areas are lacking a review but please let me know. Thanks!

[jharenza]

@komalsrathi go ahead and merge and we can more critically review the new issues as they are minor changes.

[komalsrathi]

Thanks so much!