Skip to content

Commit

Permalink
fix: skip fourDNData pairs parsing for now (2)
Browse files Browse the repository at this point in the history
  • Loading branch information
js2264 committed Jan 22, 2024
1 parent 77846c8 commit e997f31
Show file tree
Hide file tree
Showing 2 changed files with 4 additions and 4 deletions.
2 changes: 1 addition & 1 deletion Dockerfile
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ FROM bioconductor/bioconductor_docker:${BIOC_VERSION}
COPY . /opt/pkg

# Install book package
RUN Rscript -e 'repos <- BiocManager::repositories() ; remotes::install_github("lawremi/rtracklayer") ; remotes::install_local(path = "/opt/pkg/", repos=repos, dependencies=TRUE, build_vignettes=FALSE, upgrade=TRUE) ; sessioninfo::session_info(installed.packages()[,"Package"], include_base = TRUE)'
RUN Rscript -e 'repos <- BiocManager::repositories() ; remotes::install_github("lawremi/rtracklayer") ; remotes::install_github("js2264/HiContactsData") ; remotes::install_local(path = "/opt/pkg/", repos=repos, dependencies=TRUE, build_vignettes=FALSE, upgrade=TRUE) ; sessioninfo::session_info(installed.packages()[,"Package"], include_base = TRUE)'

## Build/install using same approach than BBS
RUN R CMD INSTALL /opt/pkg
Expand Down
6 changes: 3 additions & 3 deletions inst/pages/disseminating.qmd
Original file line number Diff line number Diff line change
Expand Up @@ -86,7 +86,8 @@ type of file to fetch can be specified with the `type` argument:
- `type = 'pairs'` will fetch the pairs file which was generated by the 4DN consortium and binned
into a contact matrix. Once fetched from the 4DN data portal, the local file can be imported in `R` using the `import` function, which will generate a `GInteractions` object.

```{r}
```{r eval = FALSE}
## Not evaluated for now
pairs_f <- fourDNData(experimentSetAccession = '4DNESJNPEKZD', type = 'pairs')
print(pairs_f)
import(pairs_f)
Expand All @@ -102,8 +103,7 @@ a large storage footprint.

- `type = 'insulation'` will fetch a `.bigwig` track file precomputed by the 4DN consortium. This track corresponds to the genome-wide insulation score computed by `cooltools` as described in @Crane_2015. To know more about this, read [the excerpt from 4DN data portal](https://data.4dnucleome.org/resources/data-analysis/insulation_compartment_scores#insulation_scores_and_boundaries_page_all). Once fetched from the 4DN data portal, the local file can be imported in `R` using the `import` function, which will generate a `RleList` object.

```{r eval = FALSE}
## Not evaluated for now
```{r}
library(rtracklayer)
fourDNData(experimentSetAccession = '4DNES25ABNZ1', type = 'insulation') |>
import(as = 'Rle')
Expand Down

0 comments on commit e997f31

Please sign in to comment.