fgsea tutorial issue with BiocParallel

Question

[1769mkc]

I was trying to use this fgsea library for enrichment analysis but there was this error coming up due to some issue with BiocParallel , it was resolved by adding this line register(SerialParam()) to the code .

Original source with a bit of modification

Error in registered()[[bpparamClass]] : 
  attempt to select less than one element in get1index

 

library(fgsea)
library(BiocParallel)
res <- read.csv("HSC_LSC_deseq2_CDS.txt",sep ='\t') # deseq2 output
head(res)
library(dplyr)
res2 <- res %>% 
   dplyr::select(Symbol, stat) %>% 
   na.omit() %>% 
   distinct() %>% 
   group_by(Symbol) %>% 
   summarize(stat=mean(stat))
res2
library(tidyverse)
ranks <- deframe(res2)
head(ranks, 20)
pathways.hallmark <- gmtPathways('~/mysigdb/h.all.v6.2.symbols.gmt') # files from mysigdb 
pathways.hallmark %>% 
   head() %>% 
   lapply(head)

class(pathways.hallmark)
length(pathways.hallmark)
pathways.hallmark[1]

register(SerialParam())


fgseaRes <- fgsea(pathways=pathways.hallmark, stats=ranks, nperm=1000)

fgseaResTidy <- fgseaRes %>%  as_tibble() %>% arrange(desc(NES))

fgseaResTidy %>% 
   dplyr::select(-leadingEdge, -ES, -nMoreExtreme) %>% 
   arrange(padj) %>% 
   DT::datatable()

library(ggplot2)
ggplot(fgseaResTidy, aes(reorder(pathway, NES), NES)) +
   geom_col(aes(fill=padj<0.05)) +
   coord_flip() +
   labs(x="Pathway", y="Normalized Enrichment Score",
        title="Hallmark pathways NES from GSEA") + 
   theme_minimal()

Any mistakes in the code found would be welcomed if any issues in running

Answer 1

[mark.ziemann]

I experienced the same thing just now on a not so well patched computer running an older version (R3.4.4/fgsea_1.0.2/BiocParallel_1.8.2) but tried it on another computer that I keep better updated (R3.5.2/fgsea_1.8.0/BiocParallel_1.8.2) and it worked. My advice would be to upgrade your R installation to the latest one and reinstall the packages.

[1769mkc]

yes as i updated things were broken due to one or the other dependencies ..