How can I do pathway analysis by ChipPeakAnno package?
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mehdi • 0
@0c2ae8fc
Last seen 8 days ago
Germany

when I want to do pathway analysis by ChipPeakAnno package for my chipseq data after running bellow code I face this error : ''' Error in getEnrichedPATH(peakGrangeARDMSOe4, orgAnn = "org.Hs.eg.db", : The number of gene is less than 2.Please double check your feature_id_type.''' could some one who has any idea, help me for this problem? how can I resolve this error?

library(ChipPeakAnno)
dfe4<-getEnrichedPATH(
peakGrangedf,  #this is original Grange file that I used for peak calling and annotation as well
orgAnn="org.Hs.eg.db",
pathAnn= "reactome.db",
feature_id_type = "ensembl_gene_id",
maxP = 0.01,
minPATHterm = 5,
subGroupComparison = NULL
)


this is the code that I tried and I faced mentioned error.

ChIPpeakAnno • 67 views
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Entering edit mode
mehdi • 0
@0c2ae8fc
Last seen 8 days ago
Germany

For this error I got this guidance and actually when we use our Grange file, it is better to specify the feature column to be used directly. Therefore by the following code you can get the pathway analysis output.

enriched.PATH = getEnrichedPATH(annotatedPeak**\$feature**, orgAnn="org.Hs.eg.db",

feature_id_type="ensembl_gene_id",

pathAnn="reactome.db", maxP=0.01,



Note: you will need to make sure the feature column contains the ID type specified in feature_id_type. By default, it is ensemble_gene_id. Other supported IDs are refseq_id, gene_symbol or entrez_id

by useing " ?getEnrichedPATH "in your R session you can try the examples provided by the authors.