Question: Using GenomicDataCommons R package to identify cases with both DNA methylation and gene expression data
1
gravatar for rjactonspsfcf
5 months ago by
Southampton
rjactonspsfcf80 wrote:

I'm trying to get a list of cases for which there is DNA methylation and gene expression data available for both normal and cancer tissue samples using the GenomicDataCommons R package (which I am using for the first time).

qCases <- cases() %>%
    filter( ~ samples.sample_type == "Solid Tissue Normal" | samples.sample_type == "Blood Derived Normal") %>%
    filter(~ files.type == 'gene_expression' & files.type == 'methylation_beta_value')

qCases %>% count()
> [1] 0

this returns no results

Examining the response() of qCases when only calling the first filter reveals that there are definitely cases with files that contain both gene expression and methylation beta value files.

qCases <- cases() %>%
    filter( ~ samples.sample_type == "Solid Tissue Normal" | samples.sample_type == "Blood Derived Normal") %>%
    GenomicDataCommons::select('files.type')

qCases %>% response()


> $results
> files
> 1         copy_number_segment, ----->###gene_expression###<-------, simple_somatic_mutation, 
annotated_somatic_mutation, biospecimen_supplement, clinical_supplement, biospecimen_supplement,
biospecimen_supplement, mirna_expression, aligned_reads, clinical_supplement, 
aggregated_somatic_mutation, slide_image, simple_somatic_mutation, copy_number_segment, 
clinical_supplement, clinical_supplement, biospecimen_supplement, clinical_supplement, 
clinical_supplement, clinical_supplement, biospecimen_supplement, copy_number_segment, aligned_reads, 
annotated_somatic_mutation, biospecimen_supplement, biospecimen_supplement, 
annotated_somatic_mutation, biospecimen_supplement, clinical_supplement, 
----->###methylation_beta_value###<-----, masked_somatic_mutation, simple_somatic_mutation, 
biospecimen_supplement, slide_image, copy_number_segment, annotated_somatic_mutation, 
masked_somatic_mutation, clinical_supplement, aggregated_somatic_mutation, 
aggregated_somatic_mutation, aggregated_somatic_mutation, mirna_expression, clinical_supplement, 
gene_expression, masked_somatic_mutation, gene_expression, biospecimen_supplement, aligned_reads, 
biospecimen_supplement, biospecimen_supplement, aligned_reads, simple_somatic_mutation, 
masked_somatic_mutation

My guess is that what is going wrong here is the filter is looking at individual files entries and thus no one file is both type gene_expression and type methylation_beta_value. Is there a way to filter for cases that have files with a given set of types?

I've been looking over the examples in the vignette but there don't seem to be any examples of composite queries like the one I'm trying to do. Any assistance would be appreciated!

dna methylation rna-seq gdc R • 203 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by rjactonspsfcf80
1

You may want to post on Bioconductor Support, where the GenomicDataCommons developer is more active currently.

ADD REPLYlink written 5 months ago by Kevin Blighe39k
1
gravatar for Sean Davis
5 months ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

See: https://support.bioconductor.org/p/114340/#114357 for the answer.

ADD COMMENTlink modified 5 months ago • written 5 months ago by Sean Davis25k
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