How to start with bamsignals

Question

[Lila M]

Hi everybody! I'm trying to discover new ChIP-seq tools, I'm trying bamsignals but in this tutorial fro me is not clear what is bampath and genes (and how to perform them with my data) does anyone have experience in this package and could give me his opinion or advice?

Thanks in advance!

[GenoMax]

The info is right there in the link you posted

bampath <- system.file("extdata", "randomBam.bam", package="bamsignals")
genes <-  get(load(system.file("extdata", "randomAnnot.Rdata", package="bamsignals")))

Are you not familiar with how R works?

[Lila M]

Yes, I know that , but this info is to get the "toy data" and I din't know what I need for my personal data, please, if you understand the code, could you explain what is extdata, randomAnnot.Rdata and how can I get them in my own?

Thanks

[GenoMax]

You are reading paths for randomBam.bam/randomAnnot.Rdata from a directory extdata (for package bamsignals). bampath will contain the absolute path to the bam file on your disk. extdata generally contains the raw data included with a R-package.

[Lila M]

is still not clear for me how load the BAM files and processes them, I've also tried Rsamtools but not success at all, help please!