makeInputObj2: Make the retroviral vector integration site object.

In RIPAT: Retroviral Integration Pattern Analysis Tool (RIPAT)

Description

Make an input object for annotation functions.

Usage

makeInputObj2(inDir, id, mapTool = 'blast', 
              vectorPos = 'front', outPath = getwd(), 
              outFileName = paste0('RIPAT', round(unclass(Sys.time()))))

Arguments

inDir	a string vector. Location of a directory that has a local alignment result files. All alignment result files do not include any header and comment.
id	a character vector. the specific words that can appoint alignment file names exclusively.
mapTool	a character vector. Function serves two types of file such as outputs from BLAST and BLAT. Default is 'blast'. If you want to use BLAT result, use 'blat'.
vectorPos	a character vector. Sets the position of vector on sequences. Default value is 'front'. If the vector is located at the behind of sequence, you can change it to 'behind'.
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 two types of outputs. Text file and R object. Available hit data from input is written in text file and generated as a list of GenomicRange(GR) format object.

Examples

blast_obj = makeInputObj2(inDir = system.file("scripts", package = "RIPAT"), id = 'BLASTn')
 

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