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Question: Problem with using `GRheatmapData` function in compEpiTools package
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gravatar for ma1478
6 weeks ago by
ma14780
ma14780 wrote:

Problem:

I am using the compEpiTools R package (version "1.10.0") to generate a heatmap, but I run into a problem.  The problem is when I tried using the `GRheatmapData` function, an error message appeared saying the function could not be found:

GRheatmapData(grl = grl, refgr = mycEuMycPromUnion6KbChr1, type = rep("gr",  : 
  could not find function "GRheatmapData"

It appears to me that I have loaded compEpiTools with no issues, but  could not figure out why I am getting this error.  Any idea about what would be the source of this problem?

Commands:

Here is the code I am trying to run (error message highlighted in yellow):

> library(compEpiTools)
> source('./analysisEnvironment.R')
Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
In addition: Warning message:
In readChar(con, 5L, useBytes = TRUE) :
  cannot open compressed file './data/ChIPfiles.rda', probable reason 'No such file or directory'
> mycEuMycPromPeaks= peaksRefSimple$EuMyc[1:5]
> for(i in 1:5) {
+ res= countOverlaps(mycEuMycPromPeaks[[i]], promoterGR)
+ mycEuMycPromPeaks[[i]]= mycEuMycPromPeaks[[i]][res>0]
+ }
> mycEuMycDistalPeaks= peaksRefSimple$EuMyc[1:5]
> for(i in 1:5) {
+ res= countOverlaps(mycEuMycDistalPeaks[[i]], promoterGR)
+ mycEuMycDistalPeaks[[i]]= mycEuMycDistalPeaks[[i]][res==0]
+ }
> mycEuMycPromUnion= mycEuMycPromPeaks[[1]]
> for(i in 2:length(mycEuMycPromPeaks)) mycEuMycPromUnion= union(mycEuMycPromUnion, mycEuMycPromPeaks[[i]]) # 13628
> mycEuMycPromUnion6Kb= GRsetwidth(mycEuMycPromUnion, newWidth=6000) # 3Kb upstream and downstream the mid point of each region (negative starts are corrected)
> mycEuMycPromUnion6KbChr1= mycEuMycPromUnion6Kb[seqnames(mycEuMycPromUnion6Kb)=='chr1']
> grl= c(peaksRefSimple$EuMyc[c(1:10, 16:20, 11:15, 21:25)], CGI=CGIgr) # Myc, Pol2, K4me3, K4me1, K27ac
> EuMycPromData= GRheatmapData(grl= grl, refgr = mycEuMycPromUnion6KbChr1, type= rep('gr', length(grl)), nbins= 10, txdb = txdb)
Error in GRheatmapData(grl = grl, refgr = mycEuMycPromUnion6KbChr1, type = rep("gr",  : 
  could not find function "GRheatmapData"

SessionInfo() output command:

> sessionInfo()

R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats4    parallel 
[3] stats     graphics 
[5] grDevices utils    
[7] datasets  methods  
[9] base     

other attached packages:
 [1] org.Mm.eg.db_3.4.1                     
 [2] TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2
 [3] org.Hs.eg.db_3.4.1                     
 [4] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
 [5] GenomicFeatures_1.28.5                 
 [6] compEpiTools_1.10.0                    
 [7] topGO_2.28.0                           
 [8] SparseM_1.77                           
 [9] GO.db_3.4.1                            
[10] AnnotationDbi_1.38.2                   
[11] Biobase_2.36.2                         
[12] graph_1.54.0                           
[13] BSgenome.Mmusculus.UCSC.mm9_1.4.0      
[14] BSgenome_1.44.2                        
[15] rtracklayer_1.36.4                     
[16] Biostrings_2.44.2                      
[17] XVector_0.16.0                         
[18] GenomicRanges_1.28.5                   
[19] GenomeInfoDb_1.12.2                    
[20] IRanges_2.10.3                         
[21] S4Vectors_0.14.4                       
[22] BiocGenerics_0.22.0                    

loaded via a namespace (and not attached):
 [1] methylPipe_1.10.0            
 [2] ProtGenerics_1.8.0           
 [3] bitops_1.0-6                 
 [4] matrixStats_0.52.2           
 [5] bit64_0.9-7                  
 [6] RColorBrewer_1.1-2           
 [7] httr_1.3.1                   
 [8] tools_3.4.1                  
 [9] backports_1.1.1              
[10] R6_2.2.2                     
[11] rpart_4.1-11                 
[12] KernSmooth_2.23-15           
[13] Hmisc_4.0-3                  
[14] DBI_0.7                      
[15] lazyeval_0.2.0               
[16] Gviz_1.20.0                  
[17] colorspace_1.3-2             
[18] nnet_7.3-12                  
[19] gridExtra_2.3                
[20] curl_2.8.1                   
[21] bit_1.1-12                   
[22] compiler_3.4.1               
[23] htmlTable_1.9                
[24] DelayedArray_0.2.7           
[25] caTools_1.17.1               
[26] scales_0.5.0                 
[27] checkmate_1.8.4              
[28] stringr_1.2.0                
[29] digest_0.6.12                
[30] Rsamtools_1.28.0             
[31] foreign_0.8-69               
[32] base64enc_0.1-3              
[33] dichromat_2.0-0              
[34] pkgconfig_2.0.1              
[35] htmltools_0.3.6              
[36] limma_3.32.7                 
[37] ensembldb_2.0.4              
[38] htmlwidgets_0.9              
[39] rlang_0.1.2                  
[40] RSQLite_2.0                  
[41] BiocInstaller_1.26.1         
[42] shiny_1.0.5                  
[43] BiocParallel_1.10.1          
[44] gtools_3.5.0                 
[45] acepack_1.4.1                
[46] VariantAnnotation_1.22.3     
[47] RCurl_1.95-4.8               
[48] magrittr_1.5                 
[49] GenomeInfoDbData_0.99.0      
[50] Formula_1.2-2                
[51] Matrix_1.2-10                
[52] Rcpp_0.12.12                 
[53] munsell_0.4.3                
[54] stringi_1.1.5                
[55] yaml_2.1.14                  
[56] SummarizedExperiment_1.6.4   
[57] zlibbioc_1.22.0              
[58] gplots_3.0.1                 
[59] plyr_1.8.4                   
[60] AnnotationHub_2.8.2          
[61] grid_3.4.1                   
[62] blob_1.1.0                   
[63] gdata_2.18.0                 
[64] lattice_0.20-35              
[65] splines_3.4.1                
[66] knitr_1.17                   
[67] marray_1.54.0                
[68] biomaRt_2.32.1               
[69] XML_3.98-1.9                 
[70] biovizBase_1.24.0            
[71] latticeExtra_0.6-28          
[72] data.table_1.10.4            
[73] httpuv_1.3.5                 
[74] gtable_0.2.0                 
[75] ggplot2_2.2.1                
[76] mime_0.5                     
[77] xtable_1.8-2                 
[78] AnnotationFilter_1.0.0       
[79] survival_2.41-3              
[80] tibble_1.3.4                 
[81] GenomicAlignments_1.12.2     
[82] memoise_1.1.0                
[83] cluster_2.0.6                
[84] interactiveDisplayBase_1.14.0
ADD COMMENTlink modified 6 weeks ago by mattia pelizzola200 • written 6 weeks ago by ma14780
2
gravatar for mattia pelizzola
6 weeks ago by
mattia pelizzola200 wrote:

Hi,

the method is called "heatmapData", not "GRheatmapData",

best,

mattia

ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by mattia pelizzola200

Thanks a lot for the reply!  Apparently, they might have changed the method name to `heatmapData` as for version version "1.10.0"  

ADD REPLYlink written 6 weeks ago by ma14780
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