search

robinweide / GENOVA

GENome Organisation Visual Analytics
GNU General Public License v3.0
68 stars 15 forks source link

how to create CS_discovery objsect from extrenal compartment results? #341

Open tan5251 opened 7 months ago

tan5251 commented 7 months ago

how to create CS_discovery object when using extrenal compartment results?

teunbrand commented 7 months ago

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

tan5251 commented 7 months ago

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 commented 7 months ago

Thanks. it works.