Question: goProfiles for non-model organisms with GoTermsFrame
gravatar for Maria Scheel
2.1 years ago by
Portugal / Faro / CCMAR
Maria Scheel0 wrote:

Hey there!

After completing my annotation of non-model organism with GO terms and conducting GSEA etc I wanted to compare the most differentially expressed GO terms across the three used species with the goProfiles package (Bioconductor).

I tried creating the basicProfiles with this code, which worked but deliverd zero frequencies: Cagla <- read.csv("CG_geneid_goid_test1.csv", header = T, sep="\t") Cafin.MF <- basicProfile(Cafin, idType = "GOTermsFrame", onto="MF", level=2)

The initial Cafin data frame looks like this:

GeneID Ontology Evidence GOID

1 110826457 MF IEA GO:0004888

But even if I calculated the frequencies (occurrence of GO term in data frame Cafin) manually, creating the mergedProfileList results in the error:

allcalanus.MF <-mergeProfilesLists(Cafin.MF, Cahyp.MF, Cagla.MF, profNames=c("Cafin", "Cahyp", "Cagla"))

Error in !emptyCats : invalid argument type

Can anybody help me?

ADD COMMENTlink written 2.1 years ago by Maria Scheel0
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