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Add cohort access to Ag3.snp_allele_frequencies #57

@cclarkson

Description

@cclarkson

Split from issue #51

Modify method Ag3.snp_allele_frequencies(transcript, cohorts, cohorts_analysis, ...):

  • Allow the cohorts parameter to be a dict (current behaviour continues to be supported) or a string. If a string, it must be the name of one of the columns in the cohorts dataframe.
  • Add a cohorts_analysis parameter which is a string with default value set to latest cohorts analysis. This will be used if the cohorts parameter is given as a string.
  • Other parameters left as-is.

Open questions:

  • Should this enforce a minimum sample size? Or give that as an option?

Example:

df_snp_af = ag3.snp_allele_frequencies(transcript="AGAP006028-RA", cohorts="admin1_month")
  • Use parameter name "cohort_analysis" throughout for consistency
  • Add "min_cohort_size" parameter to the snp_allele_frequencies() and gene_cnv_frequencies() method, default value 10

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