Contents

1 Available resources

RNAmodR.Data contains example data for the RNAmodR and related packages. The data is provided as gff3, fasta and bam files.

Four sets of data with multiple files are included

## snapshotDate(): 2019-10-22
library(RNAmodR.Data)
eh <- ExperimentHub()
## snapshotDate(): 2019-10-22
ExperimentHub::listResources(eh, "RNAmodR.Data")
##  [1] "RNAmodR.Data.example.fasta"     "RNAmodR.Data.example.gff3"     
##  [3] "RNAmodR.Data.example.bam.1"     "RNAmodR.Data.example.bam.2"    
##  [5] "RNAmodR.Data.example.bam.3"     "RNAmodR.Data.example.RMS.fasta"
##  [7] "RNAmodR.Data.example.RMS.gff3"  "RNAmodR.Data.example.RMS.1"    
##  [9] "RNAmodR.Data.example.RMS.2"     "RNAmodR.Data.example.AAS.fasta"
## [11] "RNAmodR.Data.example.AAS.gff3"  "RNAmodR.Data.example.bud23.1"  
## [13] "RNAmodR.Data.example.bud23.2"   "RNAmodR.Data.example.trm8.1"   
## [15] "RNAmodR.Data.example.trm8.2"    "RNAmodR.Data.example.wt.1"     
## [17] "RNAmodR.Data.example.wt.2"      "RNAmodR.Data.example.wt.3"     
## [19] "RNAmodR.Data.example.man.fasta" "RNAmodR.Data.example.man.gff3" 
## [21] "RNAmodR.Data.snoRNAdb"

These resources are grouped based on topic. Please have a look at the following man pages:

2 snoRNAdb

RNAmodR.Data.snoRNAdb consists of a table containing the published data from the snoRNAdb [@Lestrade.2006]. The can be loaded as a GRanges object.

library(GenomicRanges)
table <- read.csv2(RNAmodR.Data.snoRNAdb(), stringsAsFactors = FALSE)
## snapshotDate(): 2019-10-22
## see ?RNAmodR.Data and browseVignettes('RNAmodR.Data') for documentation
## loading from cache
head(table, n = 2)
##   hgnc_id start end hgnc_symbol modification position   guide old.transcript
## 1   53533     1 157   RNA5-8SN5           Um       14 SNORD71         U13369
## 2   53533     1 157   RNA5-8SN5            Y       55 SNORA72         U13369
##   old.start old.end old.position
## 1      6623    6779           14
## 2      6623    6779           55
# keep only the current coordinates
table <- table[,1:7]
snoRNAdb <- GRanges(seqnames = table$hgnc_symbol,
              ranges = IRanges(start = table$position, width = 1),strand = "+",
              type = "RNAMOD",
              mod = table$modification,
              Parent = table$hgnc_symbol,
              Activity = CharacterList(strsplit(table$guide,",")))
# convert to current gene name
snoRNAdb <- snoRNAdb[vapply(snoRNAdb$Activity != "unknown",all,logical(1)),]
snoRNAdb <- split(snoRNAdb,snoRNAdb$Parent)
head(snoRNAdb)
## GRangesList object of length 6:
## $RNA18SN5
## GRanges object with 69 ranges and 4 metadata columns:
##        seqnames    ranges strand |        type         mod      Parent
##           <Rle> <IRanges>  <Rle> | <character> <character> <character>
##    [1] RNA18SN5        27      + |      RNAMOD          Am    RNA18SN5
##    [2] RNA18SN5        34      + |      RNAMOD           Y    RNA18SN5
##    [3] RNA18SN5        36      + |      RNAMOD           Y    RNA18SN5
##    [4] RNA18SN5        93      + |      RNAMOD           Y    RNA18SN5
##    [5] RNA18SN5        99      + |      RNAMOD          Am    RNA18SN5
##    ...      ...       ...    ... .         ...         ...         ...
##   [65] RNA18SN5      1643      + |      RNAMOD           Y    RNA18SN5
##   [66] RNA18SN5      1678      + |      RNAMOD          Am    RNA18SN5
##   [67] RNA18SN5      1692      + |      RNAMOD           Y    RNA18SN5
##   [68] RNA18SN5      1703      + |      RNAMOD          Cm    RNA18SN5
##   [69] RNA18SN5      1804      + |      RNAMOD          Um    RNA18SN5
##                              Activity
##                       <CharacterList>
##    [1]                        SNORD27
##    [2]               SNORA50A,SNORA76
##    [3]                SNORA69,SNORA55
##    [4]                        SNORA75
##    [5]                        SNORD57
##    ...                            ...
##   [65]                        SNORA41
##   [66]                        SNORD82
##   [67] SNORD70A,SNORD70B,SNORD70C,...
##   [68]                        SNORD43
##   [69]                        SNORD20
##   -------
##   seqinfo: 9 sequences from an unspecified genome; no seqlengths
## 
## ...
## <5 more elements>

3 Sessioninfo

sessionInfo()
## R Under development (unstable) (2019-10-24 r77329)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.3 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.11-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.11-bioc/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats4    parallel  stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] RNAmodR.Data_1.1.0       ExperimentHubData_1.13.0
##  [3] AnnotationHubData_1.17.0 futile.logger_1.4.3     
##  [5] GenomicRanges_1.39.1     GenomeInfoDb_1.23.0     
##  [7] IRanges_2.21.1           S4Vectors_0.25.0        
##  [9] ExperimentHub_1.13.0     AnnotationHub_2.19.0    
## [11] BiocFileCache_1.11.0     dbplyr_1.4.2            
## [13] BiocGenerics_0.33.0      BiocStyle_2.15.0        
## 
## loaded via a namespace (and not attached):
##  [1] bitops_1.0-6                  matrixStats_0.55.0           
##  [3] bit64_0.9-7                   progress_1.2.2               
##  [5] httr_1.4.1                    tools_4.0.0                  
##  [7] backports_1.1.5               R6_2.4.0                     
##  [9] DBI_1.0.0                     tidyselect_0.2.5             
## [11] prettyunits_1.0.2             bit_1.1-14                   
## [13] curl_4.2                      compiler_4.0.0               
## [15] graph_1.65.0                  Biobase_2.47.0               
## [17] BiocCheck_1.23.0              formatR_1.7                  
## [19] DelayedArray_0.13.0           rtracklayer_1.47.0           
## [21] bookdown_0.14                 RBGL_1.63.1                  
## [23] askpass_1.1                   rappdirs_0.3.1               
## [25] stringr_1.4.0                 digest_0.6.22                
## [27] Rsamtools_2.3.0               rmarkdown_1.16               
## [29] stringdist_0.9.5.5            AnnotationForge_1.29.0       
## [31] XVector_0.27.0                rBiopaxParser_2.27.0         
## [33] pkgconfig_2.0.3               htmltools_0.4.0              
## [35] fastmap_1.0.1                 rlang_0.4.1                  
## [37] RSQLite_2.1.2                 shiny_1.4.0                  
## [39] jsonlite_1.6                  BiocParallel_1.21.0          
## [41] dplyr_0.8.3                   RCurl_1.95-4.12              
## [43] magrittr_1.5                  GenomeInfoDbData_1.2.2       
## [45] Matrix_1.2-17                 Rcpp_1.0.2                   
## [47] stringi_1.4.3                 yaml_2.2.0                   
## [49] SummarizedExperiment_1.17.0   zlibbioc_1.33.0              
## [51] biocViews_1.55.1              grid_4.0.0                   
## [53] blob_1.2.0                    promises_1.1.0               
## [55] crayon_1.3.4                  lattice_0.20-38              
## [57] Biostrings_2.55.0             GenomicFeatures_1.39.0       
## [59] hms_0.5.2                     zeallot_0.1.0                
## [61] knitr_1.25                    pillar_1.4.2                 
## [63] optparse_1.6.4                RUnit_0.4.32                 
## [65] codetools_0.2-16              biomaRt_2.43.0               
## [67] futile.options_1.0.1          XML_3.98-1.20                
## [69] glue_1.3.1                    BiocVersion_3.11.0           
## [71] evaluate_0.14                 lambda.r_1.2.4               
## [73] data.table_1.12.6             BiocManager_1.30.9           
## [75] vctrs_0.2.0                   httpuv_1.5.2                 
## [77] openssl_1.4.1                 getopt_1.20.3                
## [79] purrr_0.3.3                   assertthat_0.2.1             
## [81] xfun_0.10                     mime_0.7                     
## [83] xtable_1.8-4                  later_1.0.0                  
## [85] tibble_2.1.3                  OrganismDbi_1.29.0           
## [87] GenomicAlignments_1.23.0      AnnotationDbi_1.49.0         
## [89] memoise_1.1.0                 interactiveDisplayBase_1.25.0

4 References