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Question: Pathview: all NA's in the mapped gene data
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gravatar for Luo Weijun
4.4 years ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:
Vishal, In your example, you have to specify gene.idtype="SYMBOL" (either upper or lower case is fine here) when calling pathview function. pv.ting <- pathview(gene.data = geneV[,1], pathway.id = "05200",species = "mmu", gene.idtype="SYMBOL", out.suffix = "test2", kegg.native = T,same.layer = F) The default gene.idtype="entrez", and pathview take your input as Entrez Gene ID hence can?t map any of your gene data onto the specified pathway. Therefore, you get #FFFFFF (white) nodes, which corresponds to NA values or ?no mapped data?. If you haven?t, pathview will install the "org.Mm.eg.db" package, which is needed for mapping the gene symbol to entrez gene id. Make sure you use the official gene symbols for your data. Let me know how that goes. For details check the help page for pathview function and look under argument ?gene.idtype?. HTH. Weijun On 7/11/2013 1:59 PM, Thapar, Vishal wrote: > Hi Weijun, > > In terms of Pathview, i am having some issues. I hope you can help me here.. > > Basically, I am trying to give path view a vector with expression values and the names of the vector has the gene names. I believe that is what the function needs but its not giving me the right out put. Let me show u how: > > So this is the vector that we give in the vignette: > head(gse16873.d[, 1]) > 10000 10001 10002 10003 100048912 10004 > -0.30764480 0.41586805 0.19854925 -0.23155297 -0.04490724 -0.08756237 > > This is my vector: > head(geneV[,1]) > Upk3b Ier2 Egr1 Nkain4 Igfbp5 Slc6a4 > 2.572087 2.075237 2.725171 1.674379 3.265937 1.839275 > > This is the my command: > pv.ting <- pathview(gene.data = geneV[,1], pathway.id = "05200",species = "mmu", out.suffix = "test2", kegg.native = T,same.layer = F) > > Problem is that when we do > head(pv.out$plot.data.gene) > kegg.names labels type x y width height mol.data mol.col > 1 1029 CDKN2A gene 532 124 46 17 0.1291987 #BEBEBE > 2 51343 FZR1 gene 919 536 46 17 -0.4043256 #5FDF5F > 3 4171 MCM2 gene 553 556 46 17 -0.4202181 #5FDF5F > 4 4998 ORC1 gene 494 556 46 17 0.9864873 #FF0000 > 5 996 CDC27 gene 919 297 46 17 1.1811525 #FF0000 > 6 996 CDC27 gene 919 519 46 17 1.1811525 #FF0000 > > > when i do that for my output > head(pv.ting$plot.data.gene) > kegg.names labels type x y width height mol.data mol.col > 2 13176 Dcc gene 133 221 46 17 NA #FFFFFF > 3 12367 Casp3 gene 215 189 46 17 NA #FFFFFF > 4 12371 Casp9 gene 279 211 46 17 NA #FFFFFF > 5 12367 Casp3 gene 415 221 46 17 NA #FFFFFF > 6 12550 Cdh1 gene 133 348 46 17 NA #FFFFFF > 7 12387 Ctnnb1 gene 179 348 46 17 NA #FFFFFF > > str(pv.ting) > List of 2 > $ plot.data.gene:'data.frame': 201 obs. of 9 variables: > ..$ kegg.names: chr [1:201] "13176" "12367" "12371" "12367" ... > ..$ labels : chr [1:201] "Dcc" "Casp3" "Casp9" "Casp3" ... > ..$ type : chr [1:201] "gene" "gene" "gene" "gene" ... > ..$ x : num [1:201] 133 215 279 415 133 179 54 193 391 133 ... > ..$ y : num [1:201] 221 189 211 221 348 348 419 331 349 554 ... > ..$ width : num [1:201] 46 46 46 46 46 46 46 46 46 46 ... > ..$ height : num [1:201] 17 17 17 17 17 17 17 17 17 17 ... > ..$ mol.data : num [1:201] NA NA NA NA NA NA NA NA NA NA ... > ..$ mol.col : Factor w/ 1 level "#FFFFFF": 1 1 1 1 1 1 1 1 1 1 ... > $ plot.data.cpd :'data.frame': 13 obs. of 9 variables: > ..$ kegg.names: chr [1:13] "C00280" "C00187" "C05981" "C00165" ... > ..$ labels : chr [1:13] "C00951" "C00187" "C05981" "C00165" ... > ..$ type : chr [1:13] "compound" "compound" "compound" "compound" ... > ..$ x : num [1:13] 642 798 452 284 284 ... > ..$ y : num [1:13] 30 32 660 1164 1202 ... > ..$ width : num [1:13] 8 8 8 8 8 8 8 8 8 8 ... > ..$ height : num [1:13] 8 8 8 8 8 8 8 8 8 8 ... > ..$ kegg.names: num [1:13] NA NA NA NA NA NA NA NA NA NA ... > ..$ mol.col : Factor w/ 1 level "#FFFFFF": 1 1 1 1 1 1 1 1 1 1 ? > > So clearly there is something going one where by its not getting NA if mol.data? and the mol.col is always FFFF > > Any idea what i am doing wrong here? > > Thanks, > > Vishal
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