将 BED 文件转换为 WIG 文件

Question

Do you know any way to convert easily (either by R, or with other program) a BED file to WIG?

Can you give me some guidelines?

Answer 1

Take a look at the rtracklayer package and specifically at the following man pages:

 ?import
 ?export

Answer 2

Here is a specific example of how I would convert .bed to .wig . As @Paolo implied, it's a straight-forward procedure:

library(rtracklayer) #bioconductor

bed_loaded <- import(con="~/Downloads/my_bed.bed.gz", format="bed") #no need to unzip .gz
# bed_loaded <- import.bed(con="~/Downloads/my_bed.bed") #if you unzip 

export.wig(object=bed_loaded, con="~/Downloads/bed2wig.wig")

Note that you import and export both have methods (wig, bed, bigwig or bw, etc.). You may directly use them without specifying the method but specifying format argument.

This GitHub tutorial will be helpful.