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