makeInputObj: Make the retroviral vector integration site object.

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

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'))

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