I am trying to do KEGG analysis and I could not find the pathway data for Plasmodium falciparum in the gage package

data(kegg.sets.hs)

data(go.sets.hs)

data(carta.hs)

data(kegg.sets.mm)

data(go.sets.mm)

data(kegg.sets.rn)

data(go.sets.rn)

data(kegg.sets.sc)

data(go.sets.sc)

is there any package to provide me with relevant data for plasmodium

In gage package, you need to use function kegg.gsets() to generate gene set data:

library(gage)
kg.pfa=kegg.gsets("pfa")
kegg.gs=kg.pfa$kg.sets[kg.pfa$sigmet.idx]

note the species is pfa. pfd is not one of the 6833 species currently supported by kegg.gsets(). It is likely a recent addition to KEGG. You need to add it to korg data manually using something like:

pfd.info=c("T01051", "57267", "pfd",    "Plasmodium falciparum Dd2", "", "0", "PFDG_03934", NA, NA, NA)
data(korg)
korg=rbind(korg, pfd.info)
kg.pfd=kegg.gsets("pfd")
kegg.gs=kg.pfd$kg.sets[kg.pfd$sigmet.idx]
head(kegg.gs, 3)

note that the gene IDs look like: "PFDG_00033" "PFDG_00121" etc. make sure you are using the same type of gene ID in your expression data.

you may also try our new package SBGNview for many more pathways beyond KEGG:
GitHub
https://github.com/datapplab/SBGNview
BioC
https://bioconductor.org/packages/SBGNview/

HTHs.

Have you tried the KEGGREST package? It seems like there is some information for the desired organism in there

library(KEGGREST)
> org <- keggList("organism")
> org[grep(org[,"species"], pattern="falciparum"),]
     T.number organism species                    
[1,] "T00095" "pfa"    "Plasmodium falciparum 3D7"
[2,] "T01051" "pfd"    "Plasmodium falciparum Dd2"
[3,] "T01052" "pfh"    "Plasmodium falciparum HB3"
     phylogeny                                     
[1,] "Eukaryotes;Protists;Alveolates;Apicomplexans"
[2,] "Eukaryotes;Protists;Alveolates;Apicomplexans"
[3,] "Eukaryotes;Protists;Alveolates;Apicomplexans"

The stringDB package has GO-Term, KEGG and other enrichment analysis available for Plasmodium falciparum

https://bioconductor.org/packages/release/bioc/html/STRINGdb.html

You can also try the web-based g:profiler

https://biit.cs.ut.ee/gprofiler/gost

Plasmodium falciparum is available as organism for GO, KEGG, ... enrichment there, too.