makeExpSet: 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

makeExpSet(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 = makeExpSet(inFile = paste0(.libPaths()[1],
                                       '/RIPAT/scripts/A5_15856M_BLASTn.txt'))

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