makeInputs: Make an input table by BLAT/BLAST results

In bioinfo16/IRFinder: Vector integrated region analysis package (IRFinder)

Description

Annotation funcions in this package need specific format of inputs. So, this function converts raw data file to avaliable format of objects. In this part, user can use *BLAST* and *BLAT* output format only. About this format, check the website of BLAST and UCSC genome browser.

Usage

makeInputs(inputPath, outputPath, mapTool = 'blast', identity = 90, vectorPos = 'front')

Arguments

inputPath	a string vector. Location of a local alignment result file. When you use BLAT result file (*.psl), do not include any header and comment.
outputPath	a string vector. Location of tab-deliminated hit files.
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 file from BLAT, use 'blat'.
identity	a numeric vector. Select more proper hits by identity score. Default value is 90.
vectorPos	a character vector. Sets the position of the vector. Default value is 'front'. If the vector is located at the back, you can change it to 'behind'.

Value

Return two types of inputs. One is data table format inputs and other is GenomicRange(GR) object type.

bioinfo16/IRFinder documentation built on Aug. 19, 2019, 10:37 a.m.