Example code for mcool

[sXperfect]

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]

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]

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

[JiaxinYangJX]

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