annoByGaps: Annotate the vector integrated site by gap information from...
In bioinfo16/VVIPS: Viral Vector Integration Position Seeker

Description Usage Arguments Value

View source: R/annoByGaps.R

This function uses gap data to search the feature of integrated regions. User can get query sequence inserted in annotated gaps and distribution graphes from annotated gaps coordinations such as centromere and telomere. Plus, user can do random distribution analysis by this function.

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annoByGaps(hits, randomSet = NULL, mapTool = 'blast', organism = 'hg19', interval = 5000, range = c(-20000, 20000),
                  gapType = c('centromere', 'telomere'), outpath = '~', dbPath = paste0(.libPaths()[1], '/VVIPS/extdata'))

`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 '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.
`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).
`gapType`	a character vector. User can select annotated gap types such as centromere, telomere and heterochromatin.
`outpath`	a 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.
`dbPath`	a string vector. Directory path of database files.