I'm a bio informatics student, who is just starting with R and pathview. I normalised an expression dataset, to the point where i only have to columns (one is the gene_id, and one the fold change).
My file looks like this:
I've tried to read this into R, with this code.
> dataFC<-read.csv("D:/Users/Dani/Documents/School/OWE6B/readTopathview.csv",header = T, sep =";") > head(dataFC) > keggcode <- "sce" > data(gene.idtype.list) > gene.idtype.list > library(KEGGREST) > pathways <- keggList("pathway", keggcode) > head(pathways) > pv.out <- pathview(gene.data = dataFC, gene.idtype = "KEGG", pathway.id = "00620", species = keggcode, out.suffix = "00620", keys.align = "y", kegg.native = TRUE, key.pos = "topright")
The result however is that no genes are mapped. i get this message
Note: None of the genes or compounds mapped to the pathway!
Argument gene.idtype or cpd.idtype may be wrong.
Info: Working in directory D:/Users/Dani/Documents
Info: Writing image file sce00620.00620.png
In colnames(plot.data)[c(1, 3, 9:ncs)] = c("kegg.names", "all.mapped", :
number of items to replace is not a multiple of replacement length
How do I fix this, What am I doing wrong ( i have read the corresponsing pathview guide, but i just can't figure out why it's not working)
thanks in advance,