Question

Error:no method for coercing this S4 class to a vector

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janani.sundaresan • 0

@jananisundaresan-19303

Last seen 5.9 years ago

Hi,

I annotated my data using:

genomation_annot<-genomation::annotateWithGeneParts(chip_clean.DB, gene.parts, intersect.chr = TRUE)

this creates a S4 class object.

from what I understood, the following functions should be able to work with this object.

plotGeneAnnotation(genomation_annot, cluster = TRUE)
heatTargetAnnotation(genomation_annot, cluster = TRUE)

but insteadd I get the error message:

Error in as.list.default(X) : no method for coercing this S4 class to a vector

How can I fix this?

Thanks in advance, JS

annotation genomation • 2.0k views

ADD COMMENT • link updated 5.9 years ago by altuna akalin ▴ 20 • written 5.9 years ago by janani.sundaresan • 0

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> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

attached base packages:
 [1] grid      parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] readr_1.3.1                 genomation_1.14.0           annotatr_1.8.0              GenomicAlignments_1.18.1   
 [5] Rsamtools_1.34.0            Biostrings_2.50.2           XVector_0.22.0              edgeR_3.24.3               
 [9] limma_3.38.3                DESeq2_1.22.2               DiffBind_2.10.0             SummarizedExperiment_1.12.0
[13] DelayedArray_0.8.0          BiocParallel_1.16.2         matrixStats_0.54.0          Biobase_2.42.0             
[17] GenomicRanges_1.34.0        GenomeInfoDb_1.18.1         IRanges_2.16.0              S4Vectors_0.20.1           
[21] BiocGenerics_0.28.0        

loaded via a namespace (and not attached):
  [1] amap_0.8-16                   colorspace_1.3-2              rjson_0.2.20                  hwriter_1.3.2                
  [5] htmlTable_1.13                base64enc_0.1-3               rstudioapi_0.8                ggrepel_0.8.0                
  [9] bit64_0.9-7                   interactiveDisplayBase_1.20.0 AnnotationDbi_1.44.0          splines_3.5.2                
 [13] impute_1.56.0                 geneplotter_1.60.0            knitr_1.21                    Formula_1.2-3                
 [17] seqPattern_1.14.0             gridBase_0.4-7                annotate_1.60.0               cluster_2.0.7-1              
 [21] GO.db_3.7.0                   pheatmap_1.0.12               graph_1.60.0                  shiny_1.2.0                  
 [25] BiocManager_1.30.4            compiler_3.5.2                httr_1.4.0                    GOstats_2.48.0               
 [29] backports_1.1.3               assertthat_0.2.0              Matrix_1.2-15                 lazyeval_0.2.1               
 [33] later_0.7.5                   htmltools_0.3.6               acepack_1.4.1                 prettyunits_1.0.2            
 [37] tools_3.5.2                   bindrcpp_0.2.2                gtable_0.2.0                  glue_1.3.0                   
 [41] GenomeInfoDbData_1.2.0        Category_2.48.0               reshape2_1.4.3                systemPipeR_1.16.1           
 [45] dplyr_0.7.8                   ShortRead_1.40.0              Rcpp_1.0.0                    gdata_2.18.0                 
 [49] rtracklayer_1.42.1            xfun_0.4                      stringr_1.3.1                 mime_0.6                     
 [53] gtools_3.8.1                  XML_3.98-1.16                 AnnotationHub_2.14.2          zlibbioc_1.28.0              
 [57] scales_1.0.0                  BSgenome_1.50.0               promises_1.0.1                hms_0.4.2                    
 [61] RBGL_1.58.1                   RColorBrewer_1.1-2            BBmisc_1.11                   yaml_2.2.0                   
 [65] memoise_1.1.0                 gridExtra_2.3                 ggplot2_3.1.0                 biomaRt_2.38.0               
 [69] rpart_4.1-13                  latticeExtra_0.6-28           stringi_1.2.4                 RSQLite_2.1.1                
 [73] genefilter_1.64.0             plotrix_3.7-4                 checkmate_1.8.5               GenomicFeatures_1.34.1       
 [77] caTools_1.17.1.1              rlang_0.3.0.1                 pkgconfig_2.0.2               BatchJobs_1.7                
 [81] bitops_1.0-6                  lattice_0.20-38               purrr_0.2.5                   bindr_0.1.1                  
 [85] htmlwidgets_1.3               bit_1.1-14                    tidyselect_0.2.5              GSEABase_1.44.0              
 [89] AnnotationForge_1.24.0        plyr_1.8.4                    magrittr_1.5                  sendmailR_1.2-1              
 [93] R6_2.3.0                      gplots_3.0.1                  Hmisc_4.1-1                   DBI_1.0.0                    
 [97] pillar_1.3.1                  foreign_0.8-71                survival_2.43-3               RCurl_1.95-4.11              
[101] nnet_7.3-12                   tibble_2.0.0                  crayon_1.3.4                  KernSmooth_2.23-15           
[105] progress_1.2.0                locfit_1.5-9.1                data.table_1.11.8             blob_1.1.1                   
[109] Rgraphviz_2.26.0              digest_0.6.18                 xtable_1.8-3                  regioneR_1.14.0              
[113] httpuv_1.4.5.1                brew_1.0-6                    munsell_0.5.0                
>

ADD REPLY • link updated 5.9 years ago by James W. MacDonald 67k • written 5.9 years ago by janani.sundaresan • 0

score 0 · Answer 1 · 2019-01-12

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altuna akalin ▴ 20

@altuna-akalin-7813

Last seen 5.9 years ago

Germany/Berlin/MDC-BIMSB

try using plotTargetAnnotation()

ADD COMMENT • link 5.9 years ago altuna akalin ▴ 20

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it still gives me error. The function plotGeneAnnotation() is deprecated and s4 class coercion error still persists.

plotGeneAnnotation(genomation_annot) Error in as.list.default(X) : no method for coercing this S4 class to a vector In addition: Warning message: 'plotGeneAnnotation' is deprecated. Use 'heatTargetAnnotation ' instead. See help("Deprecated") Blockquote

ADD REPLY • link 5.9 years ago janani.sundaresan • 0

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Entering edit mode

I updated the answer, I meant plotTargetAnnotation. Could you please let me know which part of the documentation is confusing, assuming you got the idea somewhere from the docs ?

ADD REPLY • link 5.9 years ago altuna akalin ▴ 20

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Entering edit mode

I updated the answer, I meant plotTargetAnnotation. Could you please let me know which part of the documentation is confusing, assuming you got the idea somewhere from the docs ?

ADD REPLY • link 5.9 years ago altuna akalin ▴ 20