diff --git a/inst/extdata/chr17.mcool b/inst/extdata/chr17.mcool deleted file mode 100644 index 4704d15..0000000 Binary files a/inst/extdata/chr17.mcool and /dev/null differ diff --git a/inst/pages/topological-features.qmd b/inst/pages/topological-features.qmd index 64edc8f..ffe4404 100644 --- a/inst/pages/topological-features.qmd +++ b/inst/pages/topological-features.qmd @@ -39,13 +39,13 @@ into active euchromatin (A compartments) and regulated heterochromatin To investigate chromosome compartments, we will fetch a contact matrix generated from a micro-C experiment (from @Krietenstein_2020). A subset of the genome-wide -dataset is provided in the `OHCA` package. It contains intra-chromosomal +dataset is provided in the `HiContactsData` package. It contains intra-chromosomal interactions within `chr17`, binned at `5000`, `100000` and `250000` bp. ```{r} library(HiCExperiment) -library(OHCA) -cf <- fs::path_package('OHCA', 'extdata', 'chr17.mcool') +library(HiContactsData) +cf <- HiContactsData('microC', 'mcool') microC <- import(cf, resolution = 250000) microC diff --git a/inst/scripts/make_extdata.sh b/inst/scripts/make_extdata.sh deleted file mode 100644 index 8472d17..0000000 --- a/inst/scripts/make_extdata.sh +++ /dev/null @@ -1,4 +0,0 @@ -cooler dump -t chroms /home/rsg/.cache/R/fourDNData/4d434d8538a0_4DNFI9FVHJZQ.mcool::/resolutions/250000 | grep -P 'chr17\t' > inst/extdata/chromsizes -cooler dump -t pixels -r chr17 --join /home/rsg/.cache/R/fourDNData/4d434d8538a0_4DNFI9FVHJZQ.mcool::/resolutions/5000 > inst/extdata/chr17_5000.bg2 -cooler cload pairs inst/extdata/chromsizes:5000 inst/extdata/chr17_5000.bg2 -c1 1 -p1 2 -c2 4 -p2 5 -0 inst/extdata/chr17.cool -cooler zoomify --resolutions 5000,100000,250000 --balance inst/extdata/chr17.cool -o inst/extdata/chr17.mcool