calling bedtools from R

Question

[yasjas]

good morning,

is there any function to call bedtools from R rather than do it from the shell and then bring the files to R?

Thanks

[Irsan]

Instead of using bedtools you could also have a look into the GenomicRanges bioconductor library.

Answer 1

[PoGibas]

Yes, there are many ways.

You can invoke system commands using system. Or you can use fread from data.table package (adding my simple example).

library(data.table)
cmd <- "bedtools closest -a FileA -b FileB"
df <- fread(cmd)

[Neilfws]

pipe() is useful too.

[yasjas]

Thank you for your replies it worked!!!!!

[A. Domingues]

I had no idea one could use fread for that. Thanks!