Process PURPLE CNV Gene File for UMCCRISE — purple_cnv_som_gene

Processes the purple.cnv.gene.tsv file. Keeps genes that are in the UMCCR cancer gene list and selects columns of interest.

Usage

purple_cnv_som_gene_process(x, g = NULL)

Arguments

x

Path to purple.cnv.gene.tsv file.

g

Path to gene file containing at least three columns:

symbol: gene name (character).
tumorsuppressor: is this gene a tumor suppressor (TRUE/FALSE).
oncogene: is this gene an oncogene (TRUE/FALSE).

Value

List with two elements:

tab: Tibble filtered to genes found in g.
descr: Description of tibble columns.

Examples

x <- system.file("extdata/purple/purple.cnv.gene.tsv", package = "gpgr")
g <- system.file("extdata/ref/umccr_cancer_genes_2019-03-20.tsv", package = "gpgr")
(pp <- purple_cnv_som_gene_process(x, g))
#> $tab
#> # A tibble: 13 × 15
#>    gene   minCN maxCN chrom    start      end chrBand onco_or_ts transcriptID   
#>    <chr>  <dbl> <dbl> <fct>    <int>    <int> <chr>   <chr>      <chr>          
#>  1 CRBN   1.03  1.03  chr3   3150011  3179710 p26.2   ""         ENST0000023194…
#>  2 SDHA   2.01  2.01  chr5    218241   256700 p15.33  "tsgene"   ENST0000026493…
#>  3 DUSP22 2.00  2.00  chr6    292462   351353 p25.3   ""         ENST0000041923…
#>  4 IRF4   2.00  2.00  chr6    391739   411447 p25.3   "oncogene" ENST0000038095…
#>  5 FOXQ1  2.00  2.00  chr6   1312440  1314748 p25.3   ""         ENST0000029683…
#>  6 DOCK8  1.99  1.99  chr9    214865   465259 p24.3   ""         ENST0000043282…
#>  7 LARP4B 1.99  1.99  chr10   806914   931705 p15.3   "tsgene"   ENST0000061239…
#>  8 SIRT3  2.00  2.00  chr11   215458   236431 p15.5   "tsgene"   ENST0000038274…
#>  9 KDM5A  2.00  2.00  chr12   280129   389454 p13.33  "oncogene" ENST0000039978…
#> 10 ZMYM2  2.00  2.00  chr13 19958670 20091829 q12.11  ""         ENST0000061034…
#> 11 TYMS   2.01  2.01  chr18   657604   673578 p11.32  ""         ENST0000032327…
#> 12 CRLF2  0.997 0.997 chrX   1190490  1212750 p22.33  "oncogene" ENST0000040084…
#> 13 SRY    1.01  1.01  chrY   2786855  2787699 p11.2   ""         ENST0000038307…
#> # ℹ 6 more variables: minMinorAlleleCN <dbl>, somReg <dbl>, germDelReg <chr>,
#> #   minReg <dbl>, minRegStartEnd <chr>, minRegSupportStartEndMethod <chr>
#> 
#> $descr
#> # A tibble: 12 × 2
#>    Column                                                            Description
#>    <chr>                                                             <chr>      
#>  1 gene                                                              Name of ge…
#>  2 minCN/maxCN                                                       Min/Max co…
#>  3 chrom/start/end                                                   Chromosome…
#>  4 chrBand                                                           Chromosome…
#>  5 onco_or_ts                                                        oncogene (…
#>  6 transcriptID                                                      Ensembl tr…
#>  7 minMinorAlleleCN                                                  Minimum al…
#>  8 somReg (somaticRegions)                                           Count of s…
#>  9 germDelReg (germlineHomDeletionRegions / germlineHetToHomDeletio… Number of …
#> 10 minReg (minRegions)                                               Number of …
#> 11 minRegStartEnd                                                    Start/End …
#> 12 minRegSupportStartEndMethod                                       Start/end …
#>