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juanbot / CoExpNets

Co-expression network management based on WGCNA + k-means
Apache License 2.0
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Gene naming page #5

Closed juanbot closed 4 years ago

juanbot commented 5 years ago

: between the step in which we input our genes for annotation and the step in which I deliver the results of the annotation, there should be a page in the middle of the two. This page would show, for the genes you want to analyse, how many of them are not found and which network. We should give the opportunity to the user to try to go back to the previous page to try different names for the genes (sometimes genes have sinonimous names, other times genes come from different organisms)

juanbot commented 5 years ago

Sonia, I have been working on this. I have now provided two new functions reportOnGeneIDs() and reportOnGeneIDsGlobal() in CoExpNets that will help you implementing that "page in the middle" I mention in the former comment. The key for you is reportOnGeneIDsGlobal(). You will pass this function the networks, their categories, and the genes. The method will return a matrix with logical values (TRUE/FALSE). So for example, the call

ids = reportOnGeneIDsGlobal(tissue=c("PUTM","FCTX"), categories=c("10UKBEC","10UKBEC"), ids=c("TREM2","MAPTL","ENSG00000186868","nonombre"))

will return

ids TREM2 MAPTL ENSG00000186868 nonombre PUTM TRUE FALSE FALSE FALSE FCTX TRUE FALSE FALSE FALSE

As you see, each id is in a column, each network in a row. We then display this data frame as an excel sheet we can download. We highlight those genes and networks with any false values. In this same view, we include buttons for “Proceed” and “Go Back” to proceed with the analysis anyway and to go back to edit the list of genes and try again, respectively.

OK?

SoniaRuiz commented 4 years ago

Hi,

Sorry for the delay in this issue. I have implemented this middle page, which shows which genes have not been found within the networks selected: image

I didn't read your second comment on this issue until right now, so I didn't know about both 'reportOnGeneIDs()' and 'reportOnGeneIDsGlobal()' methods before implementing this middle page, sorry!

Is it enough with the information that this new implementation is providing?