annoByGene: Annotate integration sites by genes and TSSs.

Description Usage Arguments Value Examples

View source: R/annoByGene.R

Description

Annotate vector integration sites by gene data.

Usage

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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

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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.