annoByGene: Annotate the vector integrated site by genes and...

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

Description

This function uses Gene and TSS database to search the feature of integrated regions. User can get query sequence inserted in gene and distribution graphes from Gene and TSS coordinations. Plus, user can do random distribution analysis by this function.

Usage

annoByGene(hits, randomSet = NULL, 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. 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 single character. 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.
dbPath	a string vector. Directory path of database files.

Value

Return a result list constituted by insertion table (Gene), distribution table (Gene/TSS) and GRobject of Gene and TSS data.

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