annoByCpG: Annotate the vector integrated site by CpG islands.

In bioinfo16/VVIPS: Viral Vector Integration Position Seeker

Description

After load CpG island informaton from a ucsc data file, this function shows CpG island information related with vector integrated sites. User can get query sequence inserted in CpG site and distribution graph by this function.

Usage

annoByCpG(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	TRUE or FALSE. For random distribution, function makes random set, if user enter TRUE. If this value is FALSE, random distribution analysis is not executed. Default is TRUE.
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 'blat'.
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.
randomSize	an integer vector. A random set size. Default is 10000.
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.
outFile	a character vector. Attached ID to the result file name.
cpglen	an integer vector. Validate length of CpG sites in islands.
dbPath	a string vector. Directory path of database files.

Value

Return a result list is composed by insertion table, distribution table and a GenomicRange object of CpG data.

bioinfo16/VVIPS documentation built on Nov. 4, 2019, 7:20 a.m.