gravatar for dmitriylanshakov

2 hours ago by

I have problems with GOchord function in GOplot (wencke.github.io/). When I load data with ensembleID (ENSRNOG00000000007) it works fine, but when I load data with Gene Symbols (Gad1) it gives me only the first gene in chord and couldnot build the matrix. May be I should load some more libraries?

With gene Symbols:

head(chord)
immune response
RT1-CE10 1
peptide antigen assembly with MHC class II protein complex
RT1-CE10 0
regulation of protein phosphorylation response to bacterium
RT1-CE10 0 0
response to hypoxia logFC
RT1-CE10 0 0.842166

With EnsembleID:

head(chord)
immune response
ENSRNOG00000000451 1
ENSRNOG00000001480 0
ENSRNOG00000003807 0
ENSRNOG00000003869 0
ENSRNOG00000004077 0
ENSRNOG00000004089 1
peptide antigen assembly with MHC class II protein complex
ENSRNOG00000000451 0
ENSRNOG00000001480 0
ENSRNOG00000003807 0
ENSRNOG00000003869 0
ENSRNOG00000004077 0
ENSRNOG00000004089 0
regulation of protein phosphorylation
ENSRNOG00000000451 0
ENSRNOG00000001480 0
ENSRNOG00000003807 1
ENSRNOG00000003869 0
ENSRNOG00000004077 0
ENSRNOG00000004089 0
response to bacterium response to hypoxia
ENSRNOG00000000451 0 0
ENSRNOG00000001480 1 0
ENSRNOG00000003807 0 0
ENSRNOG00000003869 0 1
ENSRNOG00000004077 0 0
ENSRNOG00000004089 0 0
action potential logFC
ENSRNOG00000000451 0 5.602350
ENSRNOG00000001480 0 1.838350
ENSRNOG00000003807 0 1.439280
ENSRNOG00000003869 0 -0.545484
ENSRNOG00000004077 1 0.758108
ENSRNOG00000004089 0 -1.050340

GObar, GOBubble and GOcicrcle works fine on files with Gene Symbols.
How ensembleID's could be converted in symbols on GOChord graphs, if there is no other solution?



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