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nsheff / LOLA

Locus Overlap Analysis: Enrichment of Genomic Ranges
http://code.databio.org/LOLA
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R package error #41

Open yangyongsan-bio opened 3 years ago

yangyongsan-bio commented 3 years ago

When I replaced the background data set in the R package I run LOLA and found an error Negative b entry in table. This means either: 1) Your user sets contain items outside your universe; or 2) your universe has a region that overlaps multiple user set regions, interfering with the universe set overlap calculation. But I used the background data set of your example, but no error was reported.

fengzhanying commented 3 years ago

I get the same error, have you solved it?

nsheff commented 3 years ago

This is not an error in LOLA, it's an issue with the data you are using. In other words, the question you are asking of LOLA doesn't really make sense.

You should look carefully at your universe and how good of a fit it is for your query set. You seem to have a universe and user set that are not really similar. The algorithm used by LOLA expects that your universe is a representation of all possible regions that could have been in your universe. This expection is not satisfied in your data.

There are several ways you could address this. One option is to use the redefineUserSets() function (or the redefineUserSets argument to runLOLA) to redefine your user sets. But you should look into the results to make sure this is what you want. Another option is to change your universe to make it a better representation of your query regions.

fengzhanying commented 3 years ago

Thanks. I will check my universe to find the problems.

09Raghu09 commented 2 years ago

Hi Nathan,

I would like to highlight that in your paper named "Nonstationary Evolution and Compositional Heterogeneity in Beetle Mitochondrial Phylogenomics" you had plotted p4 results saying it groups according to the AT%. When I tried to run p4 with the dataset which you had included in the supplementary, It didn't group and the result obtained was different when I plotted for the same. It would be really helpful if you can give me a clarification. Maybe I missed something unlike you while p4 run. Could you please give a look and respond.