annoByGene: Annotate integration sites by genes and TSSs.

In bioinfo16/RIPAT: Retroviral Integration Pattern Analysis Tool (RIPAT)

Description

Annotate vector integration sites by gene data.

Usage

annoByGene(hits, ran_hits = NULL,
           mapTool = 'blast',
           organism = 'GRCh37',
           interval = 5000,
           range = c(-20000, 20000),
           outPath = getwd(),
           outFileName = paste0('RIPAT', round(unclass(Sys.time()))))

Arguments

hits	GR object. This object made by makeExpSet function.
ran_hits	GR object or list. This object is output of makeRanSet function.
mapTool	Character. Function uses two types of object from BLAST and BLAT. Default is 'blast'. If you want to use BLAT result, use 'blat'.
organism	Character. This function can run by two versions of organisms such as GRCh37, GRCh38 (Human). Default is 'GRCh37'.
interval	Integer. This number means interval number for distribution analysis. Default is 5000.
range	Integer array. The range of highlight region for analysis. Default range is c(-20000, 20000).
outPath	String. Plots are saved in this path. Default value is R home directory.
outFileName	Character. Attached ID to the result file name.

Value

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

Examples

data(blast_obj); data(gene_exam_db); data(tss_exam_db)
saveRDS(gene_exam_db, 
        paste0(system.file("extdata", package = 'RIPAT'), 
               '/GRCh37_gene.rds'))
saveRDS(tss_exam_db, 
        paste0(system.file("extdata", package = 'RIPAT'),
               '/GRCh37_TSS.rds'))

blast_gene = annoByGene(hits = blast_obj, ran_hits = NULL, 
                        outFileName = 'blast_res')

bioinfo16/RIPAT documentation built on Oct. 16, 2020, 1:39 p.m.