README updated for independent samples module #51
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Jul 13, 2021
| @@ -6,23 +6,50 @@ Many analyses that involve mutation frequencies or co-occurence require that all | |||
| However, the PBTA+GMKF data set includes many cases where multiple speciments were taken from a single individual. | |||
| This analysis creates lists of samples such that there are no cases where more than one specimen is included from each individual. | |||
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| As different analyses may require different sets of data, we actually generate a few different sets, stored in the `results` subdirectory: | |||
| As different analyses may require different sets of data, we actually generate a few different sets, stored in the `results` subdirectory. We also run the analyses based on different 'independent_level', either 'each-cohort' or 'all-cohorts'. When running with 'each-cohort', we call independent samples for each cohort+cancer_type - and same samples in different cohorts are called "independent". When running with 'all-cohorts', we call independent samples regardless of cohort or cancer_type - and same samples in different cohorts are considered the same. | |||
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Could you clarify "same samples in different cohorts"? I thought all Kids_First_Biospecimen_IDs are unique, and each Kids_First_Biospecimen_ID has only one cohort, so there cannot be any sample in different cohorts.
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@logstar, thanks Yuanchao! Sorry by "samples" I meant "participants" - I have specified above.
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Jul 13, 2021
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Thank you for the clarifications @runjin326 .
This PR looks good to me.
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Purpose/implementation Section
Update README.md file to include description of the new "each-cohort" and "all-cohorts" input args that we implemented.
What was your approach?
Paragraphs describing these two params are included.
What GitHub issue does your pull request address?
d3b-center/ticket-tracker-OPC#89
Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
Please read to see whether the description is clear enough
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
Documentation Checklist
READMEand it is up to date.analyses/README.mdand the entry is up to date.