Hi all,

I am encountering an issue when using IMAS, I really like the package so far, but I can't seem to fix this issue with the RatioFromReads function, even though it was working with the example dataset. Here is the command that gives an issue:

> Test_bam <- data.frame(rbind(c("d12_aggtctgt_trimmed_reads_1.bam","d12"),
+                              c("e04_acgcttct_trimmed_reads_1.bam","e04"),
+                              c("f03_gtcaacag_trimmed_reads_1.bam","f03")
+                              ))
> colnames(Test_bam) <- c("path", "names")

> ASdb <- RatioFromReads(ASdb=ASdb,Test_bam, "single",readLen=125, minr=3,CalIndex="IR1",Ncor=1)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘readGAlignments’ for signature ‘"integer"’

Does anybody have a clue how to solve this?

Many thanks Christophe

Session info:

> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0 IMAS_1.6.1                              IVAS_2.2.1                             
 [4] SGSeq_1.16.2                            Rsubread_1.32.2                         MASS_7.3-51.1                          
 [7] AnnotationHub_2.14.2                    alternativeSplicingEvents.hg38_1.0.1    GO.db_3.7.0                            
[10] TCGAutils_1.2.1                         GenomicDataCommons_1.6.0                magrittr_1.5                           
[13] biomaRt_2.38.0                          FirebrowseR_1.1.35                      JunctionSeq_1.12.1                     
[16] RcppArmadillo_0.9.200.7.0               Rcpp_1.0.0                              DT_0.5                                 
[19] lsmeans_2.30-0                          emmeans_1.3.2                           spatstat_1.58-2                        
[22] rpart_4.1-13                            nlme_3.1-137                            spatstat.data_1.4-0                    
[25] reshape2_1.4.3                          rmarkdown_1.11                          knitr_1.21                             
[28] IMvigor210CoreBiologies_0.1.13          BiocInstaller_1.32.1                    purrr_0.3.0                            
[31] plyr_1.8.4                              gridExtra_2.3                           dplyr_0.7.8                            
[34] GenomicAlignments_1.18.1                Rsamtools_1.34.0                        Biostrings_2.50.2                      
[37] XVector_0.22.0                          TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicFeatures_1.34.3                 
[40] AnnotationDbi_1.44.0                    readr_1.3.1                             ggplot2_3.1.0                          
[43] DESeq2_1.22.2                           SummarizedExperiment_1.12.0             DelayedArray_0.8.0                     
[46] BiocParallel_1.16.5                     matrixStats_0.54.0                      Biobase_2.42.0                         
[49] GenomicRanges_1.34.0                    GenomeInfoDb_1.18.1                     IRanges_2.16.0                         
[52] S4Vectors_0.20.1                        BiocGenerics_0.28.0                     edgeR_3.24.3                           
[55] limma_3.38.3                           

loaded via a namespace (and not attached):
  [1] utf8_1.1.4                    lme4_1.1-19                   RUnit_0.4.32                  tidyselect_0.2.5             
  [5] RSQLite_2.1.1                 htmlwidgets_1.3               devtools_2.0.1                DESeq_1.34.1                 
  [9] munsell_0.5.0                 codetools_0.2-16              statmod_1.4.30                withr_2.1.2                  
 [13] colorspace_1.4-0              ggfortify_0.4.5               highr_0.7                     rstudioapi_0.9.0             
 [17] tensor_1.5                    labeling_0.3                  GenomeInfoDbData_1.2.0        polyclip_1.9-1               
 [21] bit64_0.9-7                   rprojroot_1.3-2               xfun_0.4                      R6_2.3.0                     
 [25] doParallel_1.0.14             locfit_1.5-9.1                bitops_1.0-6                  spatstat.utils_1.13-0        
 [29] assertthat_0.2.0              promises_1.0.1                scales_1.0.0                  nnet_7.3-12                  
 [33] gtable_0.2.0                  processx_3.2.1                goftest_1.1-1                 rlang_0.3.1                  
 [37] genefilter_1.64.0             splines_3.5.2                 rtracklayer_1.42.1            lazyeval_0.2.1               
 [41] acepack_1.4.1                 checkmate_1.9.1               BiocManager_1.30.4            yaml_2.2.0                   
 [45] abind_1.4-5                   crosstalk_1.0.0               backports_1.1.3               httpuv_1.4.5.1               
 [49] Hmisc_4.2-0                   tools_3.5.2                   usethis_1.4.0                 RColorBrewer_1.1-2           
 [53] sessioninfo_1.1.1             MultiAssayExperiment_1.8.1    base64enc_0.1-3               progress_1.2.0               
 [57] zlibbioc_1.28.0               RCurl_1.95-4.11               ps_1.3.0                      prettyunits_1.0.2            
 [61] deldir_0.1-16                 cluster_2.0.7-1               fs_1.2.6                      data.table_1.12.0            
 [65] mvtnorm_1.0-8                 pkgload_1.0.2                 hms_0.4.2                     mime_0.6                     
 [69] evaluate_0.12                 xtable_1.8-3                  XML_3.98-1.16                 compiler_3.5.2               
 [73] tibble_2.0.1                  crayon_1.3.4                  minqa_1.2.4                   htmltools_0.3.6              
 [77] mgcv_1.8-26                   later_0.7.5                   Formula_1.2-3                 tidyr_0.8.2                  
 [81] geneplotter_1.60.0            DBI_1.0.0                     rappdirs_0.3.1                Matrix_1.2-15                
 [85] cli_1.0.1                     bindr_0.1.1                   igraph_1.2.2                  pkgconfig_2.0.2              
 [89] foreign_0.8-71                xml2_1.2.0                    foreach_1.4.4                 annotate_1.60.0              
 [93] estimability_1.3              rvest_0.3.2                   stringr_1.3.1                 callr_3.1.1                  
 [97] digest_0.6.18                 htmlTable_1.13.1              curl_3.3                      shiny_1.2.0                  
[101] nloptr_1.2.1                  jsonlite_1.6                  bindrcpp_0.2.2                desc_1.2.0                   
[105] fansi_0.4.0                   pillar_1.3.1                  lattice_0.20-38               httr_1.4.0                   
[109] plotrix_3.7-4                 pkgbuild_1.0.2                survival_2.43-3               interactiveDisplayBase_1.20.0
[113] glue_1.3.0                    remotes_2.0.2                 iterators_1.0.10              bit_1.1-14                   
[117] stringi_1.2.4                 blob_1.1.1                    latticeExtra_0.6-28           memoise_1.1.0