'nan' in sashimiplot PDF file

[bioPG]

rMATS software calculates the average inclusion level for a group by excluding NA values when computing IncLevelDifference. In contrast, rmats2sashimiplot issues a warning and displays 'nan' in the final PDF file when encountering NA values. Why doesn't it display the filtered mean, similar to rMATS?

[EricKutschera]

I added a branch with this commit that checks for nan when getting the group IncLevel: 51d936e

In that commit the code behaves more like the rMATS IncLevelDifference code that you mentioned: https://github.com/Xinglab/rmats-turbo/blob/v4.2.0/rMATS_P/inclusion_level.py#L51

[bioPG]

Thanks a lot for adding the branch.

[vandoorslaer]

PRMT1.SE.MATS.JC.txt
Hi,
I am trying to plot a sashimiplot for the attached SE. As you can see, all the IJC have values (no NA) yet, the sashimplots show nan for the first and last bam file for sample 1 and sample 2. When I use a grouping file, the overall IncLevel = nan.
Any idea what I may be doing wrong?
thanks!

[EricKutschera]

The file you posted has quotes around the values for IncLevel1 and IncLevel2. Those quotes should not be in the original rMATS output, but may have been added if you processed that file with another program. See this post: #110 (comment)