makeExpSet: Make the retroviral vector integration site object.

Description Usage Arguments Value Examples

View source: R/makeExpSet.R

Description

Make an input object for annotation functions.

Usage

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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

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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.