Subsetting enrichment object

[mdozmorov]

Hi Guangchuang,

The cnetplot is a really attractive feature. I wonder if it is possible to subset the enrichment object that goes into the cnetplot function?

Case scenario: Run an enrichment analysis with pvalueCutoff = 1, to see all results. Plotting them all would be infeasible. How to subset the enrichment object to, say, first ten most significant terms, and then plot it with cnetplot?

Thanks,
Mikhail

[GuangchuangYu]

> require(DOSE)
Loading required package: DOSE
DOSE v3.8.0  For help: https://guangchuangyu.github.io/DOSE

If you use DOSE in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Guang-Rong Yan, Qing-Yu He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics 2015, 31(4):608-609

> data(geneList)
> de = names(geneList)[1:100]
> x = enrichDO(de, qvalueCutoff=1, pvalueCutoff=1)
> dim(x)
[1] 383   9
> head(x, 2)
                       ID            Description GeneRatio  BgRatio
DOID:0060071 DOID:0060071 pre-malignant neoplasm      5/77  22/8007
DOID:5295       DOID:5295     intestinal disease      9/77 157/8007
                   pvalue     p.adjust       qvalue
DOID:0060071 1.671524e-06 0.0006401937 0.0004609887
DOID:5295    1.759049e-05 0.0027885022 0.0020079362
                                                  geneID Count
DOID:0060071                    6280/6278/10232/332/4321     5
DOID:5295    4312/6279/3627/10563/4283/890/366/4902/3620     9
> y = x[x$pvalue < 0.05, ]
> dim(y)
[1] 121   9
> tail(y, 2)
                 ID                    Description GeneRatio  BgRatio
DOID:7474 DOID:7474 malignant pleural mesothelioma      2/77  36/8007
DOID:8692 DOID:8692               myeloid leukemia      4/77 142/8007
              pvalue  p.adjust    qvalue             geneID Count
DOID:7474 0.04659310 0.1487096 0.1070824          10232/332     2
DOID:8692 0.04748286 0.1502970 0.1082254 820/10232/332/3620     4
> tail(x, 2)
                 ID     Description GeneRatio  BgRatio    pvalue  p.adjust
DOID:5679 DOID:5679 retinal disease      1/77 358/8007 0.9709661 0.9735079
DOID:936   DOID:936   brain disease      1/77 454/8007 0.9890750 0.9890750
             qvalue geneID Count
DOID:5679 0.7010006   4312     1
DOID:936  0.7122101   3627     1

[GuangchuangYu]

oops， y will be a data.frame.

[GuangchuangYu]

asis parameter introduced with FALSE as default value. (DOSE v >= 3.9.1)

> y = x[x$pvalue < 0.05, asis=T]
> class(y)
[1] "enrichResult"
attr(,"package")
[1] "DOSE"
> y
#
# over-representation test
#
#...@organism    Homo sapiens
#...@ontology    DO
#...@keytype     ENTREZID
#...@gene        chr [1:100] "4312" "8318" "10874" "55143" "55388" "991" "6280" "2305" ...
#...pvalues adjusted by 'BH' with cutoff <1
#...121 enriched terms found
'data.frame':   121 obs. of  9 variables:
 $ ID         : chr  "DOID:0060071" "DOID:5295" "DOID:8719" "DOID:3007" ...
 $ Description: chr  "pre-malignant neoplasm" "intestinal disease" "in situ carcinoma" "breast ductal carcinoma" ...
 $ GeneRatio  : chr  "5/77" "9/77" "4/77" "4/77" ...
 $ BgRatio    : chr  "22/8007" "157/8007" "18/8007" "29/8007" ...
 $ pvalue     : num  1.67e-06 1.76e-05 2.18e-05 1.56e-04 2.08e-04 ...
 $ p.adjust   : num  0.00064 0.00279 0.00279 0.0136 0.0136 ...
 $ qvalue     : num  0.000461 0.002008 0.002008 0.009796 0.009796 ...
 $ geneID     : chr  "6280/6278/10232/332/4321" "4312/6279/3627/10563/4283/890/366/4902/3620" "6280/6278/10232/332" "6280/6279/4751/6286" ...
 $ Count      : int  5 9 4 4 13 6 13 5 5 6 ...
#...Citation
  Guangchuang Yu, Li-Gen Wang, Guang-Rong Yan, Qing-Yu He. DOSE: an
  R/Bioconductor package for Disease Ontology Semantic and Enrichment
  analysis. Bioinformatics 2015, 31(4):608-609

[mdozmorov]

Yes, I was missing the asis = T part. Tried assigning class, and something like as. enrichResult - nothing worked. Excellent, thanks, @GuangchuangYu

[GuangchuangYu]

another solution by using dplyr verbs

[mdozmorov]

Thanks, @GuangchuangYu, the https://github.com/YuLab-SMU/clusterProfiler.dplyr functionality is a great addition! On my list to try for the next analysis.