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robinweide / GENOVA

GENome Organisation Visual Analytics
GNU General Public License v3.0
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load .hic file #340

Closed AlcaArctica closed 6 months ago

AlcaArctica commented 8 months ago

I wanted to try out this tool, but was unable to load my .hic file: I tried:

Hap1_WT_10kb_juicer <- load_contacts(
  signal_path = 'hap1.hic',
  indices_path = NULL,
  resolution = 10000,
  sample_name = NULL,
  centromeres = NULL,
  colour = NULL,
  z_norm = FALSE,
  scale_bp = 1e+09,
  scale_cis = FALSE,
  balancing = TRUE,
  legacy = FALSE,
  verbose = TRUE
)

But I am getting the error:

Reading data...
Error in utils::combn(juicer_metadata[[1]]$chrom, m = 2) : n < m

Any ideas? I was successful in visualising the .hic file with juicebox, so the file itself seems to be okay.

teunbrand commented 8 months ago

Appears to be the case that only one chromosome was found in the metadata. Have you tried the dev branch?

AlcaArctica commented 8 months ago

I installed the package with:

install.packages("remotes")
remotes::install_github("robinweide/GENOVA")
library(GENOVA)
teunbrand commented 8 months ago

You can install the dev version with remotes::install_github("robinweide/GENOVA@dev").

AlcaArctica commented 8 months ago

Thanks. This solved the error!