0-based or 1-based file format using R pipeline?

Question

[Nur]

Hello everyone,

Does anyone know that is it a problem running an R pipeline with 0-based files or should they only be in 1-based format?

Many thanks in advance!

[ATpoint]

The question is out of context. Choose the format that your package or tool expects. Like, should the book be in english, french or mandarin, well in the language you understand.

[Nur]

Thank you for your reply.

I'm working with DSS but I couldn't find any specific information regarding the file format it expects so I hesitated.

[yura.grabovska]

DSS inputs can just be text files AFAIK? What data are you starting from?

The vignette gives clear examples of the structure of input data

[Nur]

Thank you for your reply as well. I'm using BED files, which are 0-based but I often come across some information like R pipelines require inputs in 1-based file format. That made me confused a bit.

[yura.grabovska]

Nah R can read bed files in without any issues - they're just text files with extra rules. I dunno if you're maybe confusing the idea of 0/1 indexing in terms of subsetting? Subsetting/indexing in R starts from 1 not 0 so first column of a matrix would be [ ,1]

EDIT: Yeah it looks like this specifically refers to the way that genomic coordinates are stored in bed-files, rather than some file restriction. See there file spec Section 1.3

[Nur]

No, it was this input file format issue but that's a relief, thank you so much! :)