Updated analysis: independent rna sample list selection

[kgaonkar6]

What analysis module should be updated and why?

An incorrect matching here:

OpenPBTA-analysis/analyses/independent-samples/independent_rna_samples.R

Lines 46 to 49 in 6bf301e

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

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:

OpenPBTA-analysis/analyses/independent-samples/independent_rna_samples.R

Lines 46 to 49 in 6bf301e

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

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]

@logstar can you work on this?

[jharenza]

@logstar can you work on this?

[logstar]

@logstar can you work on this?

Sure. I can work on this.

[kgaonkar6]

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

[logstar]

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.