annoByRepeat: Annotate the vector integrated site by repeat sequences.

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

Description

By the repeat database, this function works for viral vector integration site annotation. User can get query sequences inserted in several types of repeats and a distribution graph by this function.

Usage

annoByRepeat(hits, randomSet, mapTool = 'blast', organism = 'hg19', interval = 5000, range = c(-20000, 20000),

Arguments

hits	a GR object. This object made from makeInputs function.
randomSet	a string vector. Type path to load a random set. If this value is null, random distribution analysis is not executed.
mapTool	a character vector. Function serve two types of file such as outputs from BLAST and BLAT. Default is 'blast'. If you want to use BLAT output, use 'blast'.
organism	a character vector. This function serves 3 versions of organisms such as hg19, hg38 (Human) and galGal6 (Chicken). Default is 'hg19'.
interval	an integer vector. This number means interval number for distribution analysis. Default is 5000.
range	an integer array. It means the range for highlight region of this analysis. Default range is c(-20000, 20000).
outpath	an string vector. Plots are saved in this path. Default value is R home directory.
repClass	a character vector or array. Users can select specific types of repeats such as SINE, LINE, DNA, RNA and Simple_repeat.
dbPath	a string vector. Directory path of database files.

Value

Return a result list constituted by insertion table, distribution table and GR object of repeat data.

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