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lgatto / pRolocGUI

Interactive visualisation and exploration of spatial proteomics data
http://lgatto.github.io/pRolocGUI
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no GO terms from getGOFromFeatures #74

Closed blue-moon22 closed 8 years ago

blue-moon22 commented 8 years ago

No errors, but empty data frame. Am I missing something?

> library("MSnbase")
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap,
    parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval,
    evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce,
    rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist, unsplit

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite
    Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: mzR
Loading required package: Rcpp
Loading required package: BiocParallel
Loading required package: ProtGenerics

This is MSnbase version 1.18.1 
  Read '?MSnbase' and references therein for information
  about the package and how to get started.

Attaching package: ‘MSnbase’

The following object is masked from ‘package:stats’:

    smooth

> library("pRoloc")
Loading required package: MLInterfaces
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: XML
Loading required package: cluster

This is MSnbase version 1.10.1 
  Read '?pRoloc' and references therein for information
  about the package and how to get started.

Warning messages:
1: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘pRoloc’ 
2: replacing previous import ‘ggplot2::alpha’ by ‘kernlab::alpha’ when loading ‘pRoloc’ 
> library("pRolocdata")

This is pRolocdata version 1.8.0.
Use 'pRolocdata()' to list available data sets.
> data("dunkley2006")
> q <- setAnnotationParams(inputs = c("Arabidopsis thaliana", "TAIR locus model"))
Using species Arabidopsis thaliana genes (TAIR10 (2010-09-TAIR10))
Using feature type TAIR locus model ID(s)
Connecting to Biomart...
**> getGOFromFeatures(featureNames(dunkley2006), params = q)
[1] tair_locus_model  go_accession      go_namespace_1003 go_name_1006      go_linkage_type  
<0 rows> (or 0-length row.names)**
> sessionInfo()
R version 3.2.4 (2016-03-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

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

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

other attached packages:
 [1] pRolocdata_1.8.0     pRoloc_1.10.1        MLInterfaces_1.50.0  cluster_2.0.3       
 [5] annotate_1.48.0      XML_3.98-1.4         AnnotationDbi_1.32.3 IRanges_2.4.8       
 [9] S4Vectors_0.8.11     MSnbase_1.18.1       ProtGenerics_1.2.1   BiocParallel_1.4.3  
[13] mzR_2.4.1            Rcpp_0.12.3          Biobase_2.30.0       BiocGenerics_0.16.1 

loaded via a namespace (and not attached):
 [1] nlme_3.1-126          pbkrtest_0.4-6        bitops_1.0-6          doParallel_1.0.10    
 [5] RColorBrewer_1.1-2    threejs_0.2.1         prabclus_2.2-6        ggvis_0.4.2          
 [9] tools_3.2.4           R6_2.1.2              affyio_1.40.0         rpart_4.1-10         
[13] mgcv_1.8-12           DBI_0.3.1             colorspace_1.2-6      trimcluster_0.1-2    
[17] nnet_7.3-12           gbm_2.1.1             preprocessCore_1.32.0 quantreg_5.21        
[21] SparseM_1.7           diptest_0.75-7        scales_0.4.0          sfsmisc_1.1-0        
[25] DEoptimR_1.0-4        mvtnorm_1.0-5         robustbase_0.92-5     randomForest_4.6-12  
[29] genefilter_1.52.1     affy_1.48.0           proxy_0.4-15          stringr_1.0.0        
[33] digest_0.6.9          minqa_1.2.4           base64enc_0.1-3       htmltools_0.3        
[37] lme4_1.1-11           rda_1.0.2-2           limma_3.26.8          htmlwidgets_0.6      
[41] RSQLite_1.0.0         impute_1.44.0         BiocInstaller_1.20.1  FNN_1.1              
[45] shiny_0.13.1          hwriter_1.3.2         mzID_1.8.0            mclust_5.1           
[49] gtools_3.5.0          car_2.1-1             dplyr_0.4.3           RCurl_1.95-4.8       
[53] magrittr_1.5          modeltools_0.2-21     Matrix_1.2-4          futile.logger_1.4.1  
[57] MALDIquant_1.14       munsell_0.4.3         vsn_3.38.0            stringi_1.0-1        
[61] MASS_7.3-45           zlibbioc_1.16.0       flexmix_2.3-13        plyr_1.8.3           
[65] grid_3.2.4            pls_2.5-0             gdata_2.17.0          lattice_0.20-33      
[69] splines_3.2.4         knitr_1.12.3          fpc_2.1-10            lpSolve_5.6.13       
[73] reshape2_1.4.1        codetools_0.2-14      biomaRt_2.26.1        futile.options_1.0.0 
[77] pcaMethods_1.60.0     lambda.r_1.1.7        mlbench_2.1-1         nloptr_1.0.4         
[81] httpuv_1.3.3          foreach_1.4.3         MatrixModels_0.4-1    gtable_0.2.0         
[85] kernlab_0.9-23        assertthat_0.1        ggplot2_2.1.0         mime_0.4             
[89] xtable_1.8-2          e1071_1.6-7           class_7.3-14          survival_2.38-3      
[93] iterators_1.0.8       rgl_0.95.1441         caret_6.0-64          sampling_2.7
blue-moon22 commented 8 years ago

Spoke too soon! Just used getAnnotationParams() and selected the same options from the list:

d <- setAnnotationParams() getGOFromFeatures(featureNames(dunkley2006), params = d)

lgatto commented 8 years ago

I think the issue is that the annotation params don't match the feature names:

> q <- setAnnotationParams(inputs = c("Arabidopsis thaliana", "TAIR locus model"))
Using species Arabidopsis thaliana genes (TAIR10 (2010-09-TAIR10))
Using feature type TAIR locus model ID(s)
Connecting to Biomart...
> getGOFromFeatures(featureNames(dunkley2006), params = q)
[1] tair_locus_model  go_accession      go_namespace_1003 go_name_1006     
[5] go_linkage_type  
<0 rows> (or 0-length row.names)

Replacing TAIR locus model by TAIR locus ID (number 8 when you create the annotation parameters interactively) yields:

> q2 <- setAnnotationParams(inputs = c("Arabidopsis thaliana", "TAIR locus ID"))
Using species Arabidopsis thaliana genes (TAIR10 (2010-09-TAIR10))
Using feature type TAIR locus ID(s)
Connecting to Biomart...
> head(getGOFromFeatures(featureNames(dunkley2006), params = q2))
  tair_locus go_accession  go_namespace_1003                   go_name_1006
2  AT1G15210   GO:0005886 cellular_component                plasma membrane
4  AT1G15210   GO:0009507 cellular_component                    chloroplast
5  AT1G15210   GO:0016020 cellular_component                       membrane
6  AT1G15210   GO:0016020 cellular_component                       membrane
7  AT1G15210   GO:0016021 cellular_component integral component of membrane
9  AT1G69460   GO:0005783 cellular_component          endoplasmic reticulum
  go_linkage_type
2             IDA
4             IDA
5             IEA
6             IDA
7             IEA
9             IDA