makeDocument: Make the result object and document.

In RIPAT: Retroviral Integration Pattern Analysis Tool (RIPAT)

Description

Rearrange the result from annotation functions.

Usage

makeDocument(res, dataType, excelOut = TRUE, 
             includeUndecided = FALSE, outPath = getwd(),
             outFileName = paste0('RIPAT', round(unclass(Sys.time()))))

Arguments

res	a GR object. This object is output of annoByGene, annoByCpG, annoByRepeat, annoByVar function.
dataType	a character vector. User enter the annotation type of input such as gene, cpg, repeat and variant.
excelOut	TRUE or FALSE. If user want to make excel file, enter TRUE. Default is TRUE.
includeUndecided	TRUE or FALSE. If user want to use undecided hits in analysis, enter TRUE. Default is FALSE.
outPath	an string vector. Plots are saved in this path. Default value is R home directory.
outFileName	a character vector. Attached ID to the result file name.

Value

Make output table and excel files about vector integration sites and proportion test result.

Examples

data(blast_gene)
makeDocument(res = blast_gene, dataType = 'gene', outFileName = 'blast_gene_res')

RIPAT documentation built on Nov. 8, 2020, 6:24 p.m.