how to create CS_discovery objsect from extrenal compartment results?

[tan5251]

how to create CS_discovery object when using extrenal compartment results?

[teunbrand]

Please see https://github.com/robinweide/GENOVA/issues/273#issuecomment-925606754

[tan5251]

I do not fullly understand it. Can you help me? here is my code: EDL <- load_contacts(signal_path ='../../hic_files/EDL.juicer.1.0.hic',resolution = 50000,sample_name = "EDL",balancing = "T",colour = "black" cs <- compartment_score(EDL) bdg <- read.table("EDL.50kb.bed",header=T) head(bdg) chrom start end EDL 1 1 0 50000 0.6647921 2 1 50000 100000 0.5358432 3 1 100000 150000 0.5442570 4 1 150000 200000 0.6440792 5 1 200000 250000 0.6039383 6 1 250000 300000 0.5219431 cs$compart_scores <-bdg pdf("2.pdf") saddle_out<- saddle(EDL,CS_discovery=cs,bins=50)

Error in [.data.table(scores, , :=(part, inverse.rle(attr(CS_discovery, : Supplied 47837 items to be assigned to 48714 items of column 'part'. If you wish to 'recycle' the RHS please use rep() to make this intent clear to readers of your code. In addition: Warning message: The 'CS_discovery' object is unsigned. It is strongly recommended that comparment scores are signed with sign_comparmentscore().

[tan5251]

Thanks. it works.