Hello,
Is there a way to get symbol instead of ENREZID in the results of GSEA(), as one can get when using readable = TRUE with enrichGO() for example?
Thank you
setReadable(gsegmt_c2, OrgDb=org.Hs.eg.db, keytype = "ENTREZID")
?setReadable
I don't manage to use setReadable on GSEA results. I guess it is not possible since it should be use on enrich() results:
setReadable {DOSE} R Documentation
setReadable
Description
mapping geneID to gene Symbol
Usage
setReadable(x, OrgDb, keytype = "auto")
Arguments
x
enrichResult Object
c2 <- read.gmt("/PathwayAnalysis/GSEA/c2.all.v5.2.entrez.gmt")
gsegmt_c2 <- GSEA(geneList=input_gseGO, exponent=1, nPerm=1000, minGSSize=10, maxGSSize=900, pvalueCutoff=0.01, pAdjustMethod="BH", TERM2GENE=c2, TERM2NAME=NA,verbose=TRUE, seed=TRUE, by="fgsea")
[1] "preparing geneSet collections..."
[1] "GSEA analysis..."
[1] "leading edge analysis..."
[1] "done..."
dim(gsegmt_c2)
[1] 1134 11
gsegmt_c2[1:2,]
ID Description setSize enrichmentScore
ACEVEDO_LIVER_CANCER_DN ACEVEDO_LIVER_CANCER_DN ACEVEDO_LIVER_CANCER_DN 526 0.3531918
ACEVEDO_LIVER_TUMOR_VS_NORMAL_ADJACENT_TISSUE_DN ACEVEDO_LIVER_TUMOR_VS_NORMAL_ADJACENT_TISSUE_DN ACEVEDO_LIVER_TUMOR_VS_NORMAL_ADJACENT_TISSUE_DN 268 0.3535863
NES pvalue p.adjust qvalues rank leading_edge
ACEVEDO_LIVER_CANCER_DN 1.350648 0.000999001 0.005652905 0.002867692 7344 tags=48%, list=35%, signal=32%
ACEVEDO_LIVER_TUMOR_VS_NORMAL_ADJACENT_TISSUE_DN 1.324621 0.000999001 0.005652905 0.002867692 7973 tags=50%, list=38%, signal=31%
core_enrichment
ACEVEDO_LIVER_CANCER_DN .../9719/55665/28992/57088/79683/8424/26017/6539/56926/7538/2203/3727/4913/5621
ACEVEDO_LIVER_TUMOR_VS_NORMAL_ADJACENT_TISSUE_DN .../8425/2203/3727/5621/2267/132884/26512/8876/120425/83452/5745/54436
setReadable(gsegmt_c2, OrgDb=org.Hs.eg.db, keytype = "auto")
Error in if (!keytype %in% kt) { : argument is of length zero
I can apply setReadable to enricher() but enricher() and GSEA() do not give the same results:
enrichment_gmt <- enricher(input_gseGO,pvalueCutoff = 0.01, pAdjustMethod = "BH", minGSSize = 10, maxGSSize = 900, qvalueCutoff = 0.01, TERM2GENE=c2, TERM2NAME=NA)
dim(enrichment_gmt)
[1] 3529 9
enrichment_gmt[1:2,]
ID Description GeneRatio BgRatio pvalue p.adjust qvalue
ENK_UV_RESPONSE_KERATINOCYTE_UP ENK_UV_RESPONSE_KERATINOCYTE_UP ENK_UV_RESPONSE_KERATINOCYTE_UP 493/7982 530/21078 5.217953e-163 2.220761e-159 2.444199e-160
HSIAO_HOUSEKEEPING_GENES HSIAO_HOUSEKEEPING_GENES HSIAO_HOUSEKEEPING_GENES 379/7982 389/21078 1.000970e-145 2.130063e-142 2.344376e-143
geneID
ENK_UV_RESPONSE_KERATINOCYTE_UP .../302/262/239/231/226/222/211/146/133/81/51/50/37/30/25
HSIAO_HOUSEKEEPING_GENES .../387/378/377/375/369/355/334/328/311/302/293/292/226/166/142/71/60/16/14/12
Count
ENK_UV_RESPONSE_KERATINOCYTE_UP 493
HSIAO_HOUSEKEEPING_GENES 379
Is there another way to use setReadable with GSEA()?
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version 2.3.6
Thank you for your help, I am getting the symbols.
this commit will give user more friendly/informative error msg and fixed the `show` method issue.