makeInputObj2 {RIPAT} | R Documentation

## Make the retroviral vector integration site object.

### 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')

[Package RIPAT version 1.4.0 Index]