Non model species using casper

reuvenieli00 commented 3 years ago

Hi,

I would like to use casper to find CN from bulk RNA-seq data of mouse and chicken.

I have followed successfully the instruction until the function "generateAnnotation". However since this command designated only for human data, I wonder if there is any alternative generic function for other species, or do I need to create this table myself in order to pass the annotation object to CreateCasperObject function.

Thanks, Eli

AnastasiaShind commented 2 years ago

I'm looking for the same option, is there a way to run casper on mouse data?

arpanda commented 2 years ago

I am also trying to use the mouse data with reference genome mm10.

As per my understanding, the current code is set to human data only. For example, generateAnnotation() function uses the below code

 if (ishg19) {
        mart <- useDataset("hsapiens_gene_ensembl", useEnsembl(biomart = "ensembl", GRCh = 37, host = host))
    } else {
        mart <- useDataset("hsapiens_gene_ensembl", useEnsembl(biomart = "ensembl", host = host))
    }

So one possible way (that I can think) is to to prepare the input data as per their annotation. Though, All columns are not self explanatory like Position, new_positions

Overall, It will be useful, if a use case on mouse data is provided.

Thanks Arijit

kenminsoo commented 1 year ago

I am also trying to use the mouse data with reference genome mm10.

As per my understanding, the current code is set to human data only. For example, generateAnnotation() function uses the below code
 if (ishg19) {
        mart <- useDataset("hsapiens_gene_ensembl", useEnsembl(biomart = "ensembl", GRCh = 37, host = host))
    } else {
        mart <- useDataset("hsapiens_gene_ensembl", useEnsembl(biomart = "ensembl", host = host))
    }
So one possible way (that I can think) is to to prepare the input data as per their annotation. Though, All columns are not self explanatory like Position, new_positions

Overall, It will be useful, if a use case on mouse data is provided.

Thanks Arijit

Based upon the code, I think similar implementation can be made for other genome. Please email me if interested and we can work to adapt it if you are still interested.

Please note I am not affilitated with the makers of this package.

knakats@emory.edu

akdess / CaSpER

Non model species using casper #67