Closed liuhankui closed 3 years ago
I guess the issue comes from check_ewce_genelist_inputs
Hey Alan, any thoughts on this one?
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I guess the issue comes from check_ewce_genelist_inputs
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Hi @liuhankui,
A requirement of Bioconductor is that no large (>5kb) data files can be included in the package submission. The workaround is to submit reference datasets to ExperimentHub. bootstrap_enrichment_test
uses reference datasets to run, for example, to check if the inputted human gene lists have mouse homologs by calling check_ewce_genelist_inputs
(as you pointed out). The relevant dataset is:
eh <- ExperimentHub::ExperimentHub()
eh[["EH5367"]])
Can I ask why you need to run EWCE offline? The reference datasets were not set up to allow local calls to ExperimentHub, see neurogenomics/ewceData/utils.R and the get_ExperimentHub
function. To rewrite EWCE and ewceData to allow localHub runs would take a significant amount of work given the necessary propagation of a parameter through all instigated EWCE functions so I would like to understand the need.
Thanks, Alan.
Hi @liuhankui,
A requirement of Bioconductor is that no large (>5kb) data files can be included in the package submission. The workaround is to submit reference datasets to ExperimentHub.
bootstrap_enrichment_test
uses reference datasets to run, for example, to check if the inputted human gene lists have mouse homologs by callingcheck_ewce_genelist_inputs
(as you pointed out). The relevant dataset is:eh <- ExperimentHub::ExperimentHub() eh[["EH5367"]])
Can I ask why you need to run EWCE offline? The reference datasets were not set up to allow local calls to ExperimentHub, see neurogenomics/ewceData/utils.R and the
get_ExperimentHub
function. To rewrite EWCE and ewceData to allow localHub runs would take a significant amount of work given the necessary propagation of a parameter through all instigated EWCE functions so I would like to understand the need.Thanks, Alan.
Hi, Alan, Thank you for explaining why the issue coming out.
The reason I run EWCE offline is that I am calculating the specificity of a large-scale sc-RNA data in local high-performance computing cluster, where has no connection of the Internet. Most of the time, I performed this kind of study on personal computer. But, as we knew, in the future there will be more and more sc-RNA data, which may require a special computing environment. Please take your time to consider the necessity of rewriting EWCE. There are several ways to figure out this issue. I have calculated the specificity matrix and transferred the matrix to personal computer and run bootstrap_enrichment_test on PC. I can also edit the check_ewce_genelist_inputs function and recompile the package and check the gene list myself. But this way may be challenging for someone who is not good at R program.
Best, Hankui.
I've created this as issue to go in our dev backlog. Thank you Hankui for pointing this out and note, we will make the change for a future release of EWCE. I'll close this issue for now but do get in touch if something else comes up.
Thanks, Alan.
This last version seems to use ExperimentHub for doing something when I perform bootstrap_enrichment_test. However, in some cases, we do not connect to the internet or cannot access the web service of bioconductor.org. Even I set ExperimentHub(localHub=T), I still not have a local cache. So, I can not use this package anymore.