annoByVar: Annotate integration sites by clinical variants.
In RIPAT: Retroviral Integration Pattern Analysis Tool (RIPAT)

Description Usage Arguments Value Examples

Annotate vector integration sites by clinical variant data.

annoByVar(hits, mapTool = 'blast', organism = 'GRCh37', interval = 5000, 
          range = c(-20000, 20000), doRandom = TRUE,
          randomSize = if(doRandom){10000}else{NULL}, 
          includeUndecided = FALSE, outPath = getwd(),
          outFileName = paste0('RIPAT', round(unclass(Sys.time()))))

`hits`	a GR object. This object made by `makeInputObj` function.
`mapTool`	a single character. Function serves two types of object such as outputs from BLAST and BLAT. Default is 'blast'. If you want to use BLAT result, use 'blat'.
`organism`	a single character. This function can run by two versions of organisms such as GRCh37, GRCh38 (Human). Default is 'GRCh37'.
`interval`	an integer vector. This number means interval number for distribution analysis. Default is 5000.
`range`	an integer array. The range of highlight region for analysis. Default range is c(-20000, 20000).
`doRandom`	TRUE or FALSE. If user types TRUE, random set is generated and user can do random distribution analysis. Default is TRUE. If this value is FALSE, random distribution analysis is not executed.
`randomSize`	an integer vector. A random set size. Default is 10000.
`includeUndecided`	TRUE or FALSE. If user want to use undecided hits in analysis, enter TRUE. Default is FALSE.
`outPath`	an string vector. Plots are saved in this path. Default value is R home directory.
`outFileName`	a character vector. Attached ID to the result file name.

Return a result list that is made up of insertion and distribution result tables and GenomicRange object of clinical variant data.

data(blast_obj); data(var_exam_db)
saveRDS(var_exam_db, paste0(system.file("extdata", package = 'RIPAT'), '/GRCh37_clinvar.rds'))

blast_clivar = annoByVar(hits = blast_obj, doRandom = FALSE, outFileName = 'blast_res')