Rename columns from API results to work with gnomeR functions
Source:R/utils-exported-helpers.R
rename_columns.RdWill return a named vector of internal column names as values and original data set names
as names as an attribute (attr(x, "names_dict"))
Examples
rename_columns(df_to_check = gnomeR::mutations)
#> # A tibble: 725 × 29
#> hugo_symbol entrez_gene_id uniqueSampleKey uniquePatientKey
#> <chr> <int> <chr> <chr>
#> 1 PARP1 142 UC0wMDAxMTI4LVQwMS1JTTM6cHJhZF9t… UC0wMDAxMTI4OnB…
#> 2 PARP1 142 UC0wMDAxODU5LVQwMS1JTTM6cHJhZF9t… UC0wMDAxODU5OnB…
#> 3 PARP1 142 UC0wMDAxODk1LVQwMS1JTTM6cHJhZF9t… UC0wMDAxODk1OnB…
#> 4 AKT1 207 UC0wMDAxMTI4LVQwMS1JTTM6cHJhZF9t… UC0wMDAxMTI4OnB…
#> 5 AKT1 207 UC0wMDAxODQ1LVQwMS1JTTM6cHJhZF9t… UC0wMDAxODQ1OnB…
#> 6 AKT1 207 UC0wMDA1NTcwLVQwMS1JTTU6cHJhZF9t… UC0wMDA1NTcwOnB…
#> 7 ALK 238 UC0wMDAxNzY4LVQwMS1JTTM6cHJhZF9t… UC0wMDAxNzY4OnB…
#> 8 ALK 238 UC0wMDA0NTA4LVQwMS1JTTU6cHJhZF9t… UC0wMDA0NTA4OnB…
#> 9 ALK 238 UC0wMDAxODk1LVQwMS1JTTM6cHJhZF9t… UC0wMDAxODk1OnB…
#> 10 ALK 238 UC0wMDAyOTg0LVQwMS1JTTM6cHJhZF9t… UC0wMDAyOTg0OnB…
#> # ℹ 715 more rows
#> # ℹ 25 more variables: molecular_profile_id <chr>, sample_id <chr>,
#> # patient_id <chr>, study_id <chr>, center <chr>, mutation_status <chr>,
#> # validation_status <chr>, start_position <int>, end_position <int>,
#> # reference_allele <chr>, hgv_sp_short <chr>, variant_classification <chr>,
#> # functionalImpactScore <chr>, fisValue <dbl>, linkXvar <chr>, linkPdb <chr>,
#> # linkMsa <chr>, ncbi_build <chr>, variant_type <chr>, keyword <chr>, …
x <- rename_columns(df_to_check = gnomeR::sv)
attr(x, "names_dict")
#> sample_id patient_id
#> "sampleId" "patientId"
#> study_id molecular_profile_id
#> "studyId" "molecularProfileId"
#> ncbi_build site_1_hugo_symbol
#> "ncbiBuild" "site1HugoSymbol"
#> site_2_hugo_symbol site_2_effect_on_frame
#> "site2HugoSymbol" "site2EffectOnFrame"
#> sv_status dna_support
#> "svStatus" "dnaSupport"
#> rna_support comments
#> "rnaSupport" "comments"
#> event_info site_1_entrez_gene_id
#> "eventInfo" "site1EntrezGeneId"
#> site_1_ensembl_transcript_id site_1_chromosome
#> "site1EnsemblTranscriptId" "site1Chromosome"
#> site_1_position site_1_contig
#> "site1Position" "site1Contig"
#> site_1_region site_1_region_number
#> "site1Region" "site1RegionNumber"
#> site_1_description site_2_entrez_gene_id
#> "site1Description" "site2EntrezGeneId"
#> site_2_ensembl_transcript_id site_2_chromosome
#> "site2EnsemblTranscriptId" "site2Chromosome"
#> site_2_position site_2_contig
#> "site2Position" "site2Contig"
#> site_2_region site_2_region_number
#> "site2Region" "site2RegionNumber"
#> site_2_description class
#> "site2Description" "variantClass"