convertInputData: The R function for converting Genomic Ranges data structure...

In chromDraw: chromDraw is a R package for drawing the schemes of karyotypes in the linear and circular fashion.

Description

The R function for converting Genomic Ranges data structure to the chromDraw dat format. Output of this function is file "data.txt" in the working directory.

Usage

convertInputData(karyotypes)

Arguments

karyotypes

vector of the Genomic Ranges structures per karyotype.

Value

return exit state.

Examples

#load package
library(GenomicRanges)

#data generating
karyotype1 <- GRanges(seqnames =Rle(c("Ack1", "Ack2"), c(5, 5)),ranges = 
IRanges(start = c(0, 400000,0,3300000,6000000,0,2500000,0,3800000,6400000), 
        end = c(400000,3300000,0,6000000,10400000,2500000,3800000,0,6400000,14800000), 
        names = c("A","B","CENTROMERE","C","D","E","F","CENTROMERE","G","H")),  
        color = c("orange","yellow","","orange","red","green","green","","red","orange"));

karyotype2 <- GRanges(seqnames =Rle(c("Ack3", "Ack4"), c(4, 4)),ranges = 
IRanges(start = c(0,0, 2400000,3500000,0,0,2400000,6700000), 
        end = c(2400000,0,3500000,12200000,2400000,0,6700000,9200000), 
        names = c("I","CENTROMERE","J","K","L","CENTROMERE","M","N")), 
        color = c("light_blue","","orange","red","pink","","red","light_blue"));

inputData <- list(karyotype1,karyotype2);

#run the function for generate chromDraw data file.
convertInputData(inputData);

chromDraw documentation built on Nov. 8, 2020, 5:30 p.m.