Example code for mcool - Githubissues

sXperfect commented 1 year ago

Hello,

I tried to run FLAMINGO on mcool data with the following code

library(FLAMINGOr)
library(GenomicFeatures)
library(Matrix)
all_size <- getChromInfoFromUCSC("hg38")
chr_name = '1'
chr_name = as.numeric(chr_name)
chr_size = all_size[chr_name,2]
chr_name <- paste0('chr',chr_name)
res = flamingo.main_func_large(
                         hic_data_low='4DNFI3PNAYBK.mcool',
                         file_format='mcool',
                         domain_res=1e6,
                         frag_res=5e3,
                         chr_size=chr_size,
                         chr_name=chr_name,
                         normalization='KR',
                         downsampling_rates=0.75,
                         lambda=10,
                         max_dist=0.01,
                         nThread=8
                         )

I only changed the hic_data_low an the file_format according to the README file but I always encounter error as follows:

Error in Matrix::sparseMatrix(i = csr_rawcount[, 1], j = csr_rawcount[,  : 
  'dims' must contain all (i,j) pairs

What might be the cause?

JiaxinYangJX commented 1 year ago

Thanks for using our software! We are trying to make the script for mcool files more flexible.

In addition, we are currently collecting all the feedback and reorganizing our tools. We will release a more user-friendly version by next month.

lucasphilipp1 commented 11 months ago

I am experiencing this problem as well using a different mcool file.

JiaxinYangJX commented 9 months ago

Hi @sXperfect @lucasphilipp1 Thanks for using our tools! We just released a lite version of FLAMINGO, which is faster, more memory-efficient, and more user-friendly. We fixed the majority of bugs and hope the new version could help. Below is the link. https://github.com/JiaxinYangJX/FLAMINGOrLite

wangjr03 / FLAMINGO

Example code for mcool #10