makeInputObj {RIPAT} | R Documentation

## Make the retroviral vector integration site object.

### Description

Make an input object for annotation functions.

### Usage

    makeInputObj(inFile, mapTool = 'blast',
                 vectorPos = 'front', outPath = getwd(),
                 outFileName = paste0('RIPAT', round(unclass(Sys.time()))))

### Arguments

`inFile` | a string vector. The path of a local alignment result file. File do not include any header and comment.
`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 = makeInputObj(inFile = paste0(.libPaths()[1], '/RIPAT/scripts/A5_15856M_BLASTn.txt'))

[Package RIPAT version 1.2.0 Index]