Updated GSVA module to include cancer_group comparison #299
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| if(harmonized_diagnosis_n>=2){ | ||
| #if(harmonized_diagnosis_n>=2){ |
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@sangeetashukla, Why are you removing >2 cutoffs?
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To be honest, we can probably remove harm dx from this altogether....just keep broad hist and the cancer groups?
| if(harmonized_diagnosis_n>=2){ | ||
| #if(harmonized_diagnosis_n>=2){ |
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@sangeetashukla, Why are you removing >2 cutoffs?
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|
Check to confirm that missing results are due to not meeting the cutoff.
Not to remove them.
There are also issues with the comparison column. You can hold on until I
complete reviewing.
…On Wed, Jan 4, 2023 at 7:56 AM Sangeeta Shukla ***@***.***> wrote:
***@***.**** commented on this pull request.
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In analyses/gene-set-enrichment-analysis/02-model-gsea.Rmd
<#299 (comment)>
:
> - if(harmonized_diagnosis_n>=2){
+ #if(harmonized_diagnosis_n>=2){
@ewafula <https://github.com/ewafula> The issue description requires
"Check to confirm that ... all harmonized diagnosis ANOVA statistics *don't
meet* the >2 cutoffs". Am I missing something? On the other hand, as
@jharenza <https://github.com/jharenza> suggests, I can go ahead and
remove harm_dx altogether, keeping broad_hist and cancer_group.
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Thank you for @sangeetashukla working on this!
@jharenza, I have updated the PR to exclude harmonized_diagnosis and include `broad_histology.
Questions:
- Should the module be updated to include other cohorts? Currently subsetting for only PBTA
- PBTA's
broad_histologycolumn includes terms such asNon-tumorandOther,which are being used as a level factor for the predictor variable (broad_histology inANOVAand the post-hoc test,TukeyHSDtests. Should they be filtered out from histology files before the statistical tests are run?
Yes, should do all here
Yes, we can remove |
@jharenza, I am assuming we need to filter for tumor samples only, which is currently not implemented in the code. Do we also include adult tumors in the TCGA cohort? |
Yes, tumor only (exclude gtex, should not have much normal RNA-Seq in other cohorts). We can leave TCGA out for now |
Purpose/implementation Section
Update gene-set-enrichment-analysis module
What scientific question is your analysis addressing?
harmonized_diagnosisand includebroad_histologyin addition tocancer_groupand predictor variablesWhat GitHub issue does your pull request address?
Issue 455
Is there anything that you want to discuss further?
No.
Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?
Yes
Results
What types of results are included (e.g., table, figure)?
gsva_anova_exome_capture_cancer_group.tsv
gsva_anova_polya_broad_histology.tsv
gsva_anova_polya_cancer_group.tsv
gsva_anova_polya_stranded_broad_histology.tsv
gsva_anova_polya_stranded_cancer_group.tsv
gsva_anova_stranded_broad_histology.tsv
gsva_anova_stranded_cancer_group.tsv
gsva_scores.tsv
gsva_tukey_exome_capture_cancer_group.tsv
gsva_tukey_polya_broad_histology.tsv
gsva_tukey_polya_cancer_group.tsv
gsva_tukey_polya_stranded_broad_histology.tsv
gsva_tukey_polya_stranded_cancer_group.tsv
gsva_tukey_stranded_broad_histology.tsv
gsva_tukey_stranded_cancer_group.tsv
Reproducibility Checklist
Documentation Checklist
READMEand it is up to date.analyses/README.mdand the entry is up to date.