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AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project
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Updated analysis: independent rna sample list selection #1103

Open kgaonkar6 opened 3 years ago

kgaonkar6 commented 3 years ago

What analysis module should be updated and why?

An incorrect matching here: https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/6bf301eea42a7f8812c3b14cee35a961097f8ecf/analyses/independent-samples/independent_rna_samples.R#L46-L49

The filtered rnaseq samples histology_df above will not have any dna biospecimen ids that match so it will be an empty dataframe.

What changes need to be made? Please provide enough detail for another participant to make the update.

The code here: https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/6bf301eea42a7f8812c3b14cee35a961097f8ecf/analyses/independent-samples/independent_rna_samples.R#L46-L49

should actually map to Kids_First_Participant_ID

 independent_dna <- histology_df %>%
    # include matched independent_dna samples
    dplyr::filter(Kids_First_Participant_ID %in%
                    independent_dna_sample_df$Kids_First_Participant_ID)

What input data should be used? Which data were used in the version being updated?

pbta-histologies.tsv

When do you expect the revised analysis will be completed?

~1/2 day

Who will complete the updated analysis?

@kgaonkar6

jharenza commented 3 years ago

@logstar can you work on this?

jharenza commented 3 years ago

@logstar can you work on this?

logstar commented 3 years ago

@logstar can you work on this?

Sure. I can work on this.

kgaonkar6 commented 3 years ago

This is low priority @logstar so I think you can move this from your to-do list for now.

logstar commented 3 years ago

This is low priority @logstar so I think you can move this from your to-do list for now.

Thank you for letting me know @kgaonkar6 ! I will work on this after finishing some ongoing PedOT work.