rundNdS: Perform dN/dS analysis on a set of mutations from multiple...

In J0bbie/R2CPCT: Misc. functions to perform import and analysis of WGS and RNA-Seq samples

Description

Perform dN/dS analysis on a set of mutations from multiple CPCT-02 samples.

Usage

rundNdS(dataMuts)

Arguments

dataMuts

(VRanges): VRanges containing the mutations which will be inputted into dN/dS.

Details

The dNdS database was made from ENSEMBL v104 (GENCODE v38) using the following code and following the dN/dS buildref vignette:

# Remove non-standard chromosomes, clone-based genes and CDS which cannot be divided by 3. ENSEMBLv104 <- readr::read_tsv('~/test/mart_export.txt') dplyr::filter(!grepl('_', 'Chromosome/scaffold name')) dplyr::filter('CDS Length' dplyr::filter(!is.na('Genomic coding start')) dplyr::filter(!grepl('^AC[0-9]', 'Gene name')) dplyr::filter(!grepl('^AP00|^RP11-', 'Gene name')) dplyr::filter(!grepl('\.', 'Gene name')) dplyr::select( 'gene.id' = 'Gene stable ID', 'gene.name' = 'Gene name', 'cds.id' = 'Protein stable ID', 'chr' = 'Chromosome/scaffold name', 'chr.coding.start' = 'Genomic coding start', 'chr.coding.end' = 'Genomic coding end', 'cds.start' = 'CDS start', 'cds.end' = 'CDS end', 'length' = 'CDS Length', 'strand' = Strand)

write.table(ENSEMBLv104, file = '~/test/mart_export_filtered.txt', sep = '\t', row.names = FALSE, quote = FALSE)

# Generate refCDS database. pathCDS = '~/test/mart_export_filtered.txt' pathFasta = '/mnt/onco0002/repository/general/genomes/hsapiens/hg19_HMF/Homo_sapiens.GRCh37.GATK.illumina.fasta' dndscv::buildref(cdsfile = pathCDS, genomefile = pathFasta, outfile = 'inst/extdata/refCDS_ENSEMBLv104_HMF.rda', excludechrs='MT', useids = TRUE)

Value

(tibble) Returns a tibble of the dNdS results.

Examples

 data.Cohort <- R2CPCT::importWGSOfCohort(<cpctIds>, <combinedData>)
 rundNdS(data.Cohort$somaticVariants)

J0bbie/R2CPCT documentation built on Feb. 24, 2022, 8:15 a.m.