R: Combine fragments below certain length - r

Question

I have a bed file containing restriction fragments of the mouse genome. Each fragment has a different length/width, like this:
chr start end width
1 chr1 0 3000534 3000534
2 chr1 3000535 3000799 264
3 chr1 3000800 3001209 409
4 chr1 3001210 3001496 286
5 chr1 3001497 3002121 624
Is it possible to combine shorter fragments ( < 500bp) with adjacent fragments using R (see example below) and if yes how?
chr start end width
1 chr1 0 3000534 3000534
2 chr1 3000535 3001209 673
3 chr1 3001210 3002121 910
Note, I don't want to filter out fragments under a certain length, so sub setting the data is not an option.
I hope my question is not too confusing…

Answer 1

Here is a first solution, that supposes that chr stays the same and that filters out the last fragment if it is < 500 (the result is the dataframe you put in your example) :
mydata<-data.frame(chr=rep("chr1",6),start=c(0,3000535,3000800,3001210,3001497,3002122),end=c(3000534,3000799,3001209,3001496,3002121,3002134),width=c(3000534,264,409,286,624,12),stringsAsFactors=F)
i<-1
while(i<nrow(mydata)){
if(mydata$width[i]>=500) {
i<-i+1
} else {
mydata$end[i]<-mydata$end[i+1]
mydata$width[i]<-sum(mydata$width[i:(i+1)])
mydata<-mydata[-(i+1),]
}
}
if(mydata$width[i]<500) mydata<-mydata[-i,]