annoByRepeat: Annotate integration sites by repeats and microsatellites.

Description Usage Arguments Value Examples

View source: R/annoByRepeat.R

Description

Annotate vector integration sites by repeat and microsatellite data.

Usage

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annoByRepeat(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()))))

Arguments

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.

Value

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

Examples

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data(blast_obj); data(repeat_exam_db); data(micro_exam_db)
saveRDS(repeat_exam_db, paste0(system.file("extdata", package = 'RIPAT'), '/GRCh37_repeat.rds'))
saveRDS(micro_exam_db, paste0(system.file("extdata", package = 'RIPAT'), '/GRCh37_microsat.rds'))

blast_repeat = annoByRepeat(hits = blast_obj, doRandom = FALSE, outFileName = 'blast_res')

RIPAT documentation built on Nov. 8, 2020, 6:24 p.m.