some funcitions can not be found

[Solipugids]

I found that some functions, get_encode_types & get_schemas could not be found in current version of ENCODExplorer. But these functions were listed in the official manual.

I did not check the rest functions in the packadge. But it is nessasary to add these features as the encode_df data is too old and needs to be updated.

Thanks you.

[CharlesJB]

Hello,

While those functions (get_encode_types and get_schemas) are documented, they are not exported. The documentation was mostly meant for developpers.

You can still call them this way:

ENCODExplorer:::get_encode_types()
ENCODExplorer:::get_schemas()

But I tested it to make sure and you should be able to update the database as mentioned in the vignette:

database_filename = "new.encode.rda"
tables = prepare_ENCODEdb(database_filename)
new_encode_df <- export_ENCODEdb_matrix(tables)

I'm currently working to make sure the package pass all the checks, but I should also push an updated version in the github soon.

[Solipugids]

Hi CharlesJB,

Thanks for your considerate explaion. Yes, I found the function could be called by the above ways. And I also tried the function for updating data in vignette. It all worked. But I still have an issue. The issue was that the data was still incomplete after I updated. Some of the experiments records were empty by the accession number, such as "ENCSR254YRM", "ENCSR847DIT", which could be queried from experiments matrix in ENCODE portral. So how could I synchronized the data with ENCODE (www.encodeproject.org) when necesary?

[CharlesJB]

I did some checks and this is clearly a bug because the two datasets you mention are in the new_encode_df object:

> sum(new_encode_df$accession == "ENCSR254YRM")
[1] 42
> sum(new_encode_df$accession == "ENCSR847DIT")
[1] 60

I will look into this and push the fix as soon as possible.

Thank you for reporting it.

[CharlesJB]

The fixes are now pushed on the github. I'm having some problem with the new git infrastructure of Bioconductor, so it could take a few days before it gets fixed on the official Bioconductor repositories.

Meanwhile, you can install the github version with devtools:

library(devtools)
install_github("CharlesJB/ENCODExplorer")