How to export the output list of csCluster( ) from CummeRbund?

Question

[LuisNagano]

I'm a beginner in bioinformatics and I have a question about how to export the output list of my csCluster () from CummeRbund? So that I can analyze a specific gene cluster that was generated. I haven't found how to do this in the CummeRbund manual.

Thanks

Answer 1

[domenico.somma]

Hi there, I have the same issue. I tried:

> write.csv(ic)
Error in pam(x = n, k = k) : could not find function "pam"

but didn't work. On cummeRbund manual there is:

csCluster Returns a ggplot2 plot object with geom_line layer plotting FPKM values over conditions faceted by k-means clustering clusters.

so I tried:

ggsave("prova",plot=ic,device=pdf)
Saving 7 x 7 in image
Error in UseMethod("grid.draw") : 
no applicable method for 'grid.draw' applied to an object of class "list"

Can anyone help?

Answer 2

[domenico.somma]

I found a workaround. If you are using Rstudio:

options(max.print=1000000)

and then just:

capture.output(data,file="export.txt")

That's all. Not much pro, but worked for me

Answer 3

[Gabby]

enter code hereto export the list of cluster and corresponding gene list :

clusterinfo=ic[["clustering"]]

write.table(clusterinfo2,"file.tsv", sep="\t")