This repository has been archived by the owner on Jun 16, 2023. It is now read-only.
-
Notifications
You must be signed in to change notification settings - Fork 0
Updated analysis: independent-samples module #89
Comments
5 tasks
5 tasks
The code and results are updated in d3b-center/OpenPedCan-analysis#48. The README.md needs to be updated for the each-cohort procedure. We would probably need to clarify that in |
@runjin326 can you work on this? |
@jharenza, absolutely! I will do that :) |
3 tasks
The README.md is updated in d3b-center/OpenPedCan-analysis#51. |
Sign up for free
to subscribe to this conversation on GitHub.
Already have an account?
Sign in.
What analysis module should be updated and why?
The
independent-samples
module needs to be updated for the following purposes.cohort
and also bycancer_group
. Output a merged table for each (experimental_strategy
,primary/primary-plus/relapse
) like before.The reason for this update is that certain primary samples are not captured if we use all samples for creating the lists. Certain patients have primary samples in different
cohorts
, so only one cohort of their primary samples will be randomly retained in previous lists. For example,(Update Fri Jul 2 15:27:11 2021 by YZ) The not-captured GMKF Neuroblastoma primary samples might be causing the ALK mutation frequency discrepancy between PediatricOpenTargets and pedcbio, as described by @jharenza at d3b-center/OpenPedCan-analysis#45 (review)
Update
experimental_strategy
to%in% c("WGS", "WXS", "Targeted Sequencing")
in01-generate-independent-specimens.R
and00-repeated-samples.Rmd
. In v6 release,"Targeted Sequencing", "Targeted-Capture"
are harmonized to"Targeted Sequencing"
, as requested in histologies.tsv experimental_strategy update #62Update
tumor_descriptor
inindependent-samples.R
andindependent_rna_samples.R
to the following. The changes are requested in histologies.tsv tumor_descriptor update #61What changes need to be made? Please provide enough detail for another participant to make the update.
Run the same procedure on each
cohort
andcancer_group
. Includecohort
andcancer_group
fields in the result lists. Combine all result lists into one list.Update
experimental_strategy
andtumor_descriptor
where they are used.What input data should be used? Which data were used in the version being updated?
histologies.tsv
, which is updated in v6.When do you expect the revised analysis will be completed?
1-3 days.
Who will complete the updated analysis?
@runjin326
cc: @jharenza
The text was updated successfully, but these errors were encountered: