Get all Coding SSMs — get_all_coding

Retrieve all coding SSMs from GAMBL in MAF-like format, regardless of seq_type.

Usage

get_all_coding_ssm(these_samples_metadata = NULL, include_silent = FALSE, ...)

Arguments

these_samples_metadata: Supply a metadata table containing the sample/seq_type combinations you want.
include_silent: If set to TRUE, silent/synonymous mutations in the coding regions will also be returned.
...: Additional arguments passed to get_coding_ssm

Value

A data frame containing all the MAF data columns (one row per mutation).

Details

Effectively retrieve coding SSM calls from one or all DNA seq_type. For additional optional arguments, see get_coding_ssm

Examples

my_meta = suppressMessages(get_gambl_metadata())
maf_all_seqtype = get_all_coding_ssm(my_meta)

table(maf_all_seqtype$maf_seq_type)
#> 
#> capture  genome 
#> 1214014  248643 

# most common mutations by gene and Variant_Classification
dplyr::group_by(maf_all_seqtype,Hugo_Symbol,Variant_Classification) %>% 
  dplyr::count() %>% 
  dplyr::arrange(desc(n))
#> genomic_data Object
#> Genome Build: grch37 
#> Showing first 10 rows:
#>    Hugo_Symbol Variant_Classification    n
#> 1      IGLV3-1      Missense_Mutation 2952
#> 2     IGHV2-70      Missense_Mutation 2787
#> 3          TTN      Missense_Mutation 2474
#> 4         BCL2      Missense_Mutation 2120
#> 5         BCL2                 Silent 2120
#> 6        IGLL5      Missense_Mutation 1888
#> 7     IGHV1-69      Missense_Mutation 1570
#> 8         PIM1      Missense_Mutation 1180
#> 9        MUC16      Missense_Mutation 1172
#> 10       IGLL5                 Silent 1135