integPatternByChr: Retroviral integration pattern on chromosomes

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

Description

Check retroviral integration pattern on chromosomes

Usage

integPatternByChr(hits, ran_hits, excelOut = TRUE,
                  isExpList = FALSE, isRanList = FALSE,
                  outPath = getwd(),
                  outFileName = paste0('RIPAT', round(unclass(Sys.time()))))

Arguments

hits	a GR object or list. This object made by makeInputObj function.
ran_hits	a GR object or list. This object is output of ranSetGenerator function.
excelOut	TRUE or FALSE. If user want to make excel file, enter TRUE. Default is TRUE.
isExpList	TRUE or FALSE. If hits is the list of several experimental data, enter TRUE. Default is FALSE.
isRanList	TRUE or FALSE. If ran_hits is the list several random data, enter TRUE. Default is FALSE.
outPath	a string vector. Directory path of tab-deliminated hit files generated by this function.
outFileName	a character vector. Attached character to the result file name.

Value

Return a result list that is made up of table(s) about
experimental/random data integration frequency on chromosomes.

Examples

data(blast_obj)
chrCheck = integPatternByChr(hits = blast_obj)
 

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