could not find function "getAlternativePromoters"

[wenmm]

I successfully run the proActiv function and then according to pipeline(https://goekelab.github.io/proActiv/articles/proActiv.html#running-proactiv) I run getAlternativePromoters there occurs the error that:
Error in getAlternativePromoters(result = result, referenceCondition = "Control") :
could not find function "getAlternativePromoters"

[jleechung]

Hi @wenmm, thanks for your interest in proActiv!

Can you check what version of proActiv you are running with packageVersion('proActiv')?
Any version above 1.1.18 should have getAlternativePromoters.

You can test with the following code (from the vignette):

library(proActiv)

files <- list.files(system.file('extdata/vignette/junctions', 
                                package = 'proActiv'), full.names = TRUE)

promoterAnnotation <- promoterAnnotation.gencode.v34.subset

condition <- rep(c('A549', 'HepG2'), each=3)

result <- proActiv(files = files,
                   promoterAnnotation = promoterAnnotation,
                   condition = condition)

alternativePromoters <- getAlternativePromoters(result = result, referenceCondition = "A549")

Session info:

> sessionInfo()`
R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)

Matrix products: default

locale:
[1] LC_COLLATE=English_Singapore.utf8  LC_CTYPE=English_Singapore.utf8    LC_MONETARY=English_Singapore.utf8
[4] LC_NUMERIC=C                       LC_TIME=English_Singapore.utf8    

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

other attached packages:
[1] proActiv_1.6.0

loaded via a namespace (and not attached):
 [1] bitops_1.0-7                matrixStats_0.62.0          bit64_4.0.5                 filelock_1.0.2             
 [5] RColorBrewer_1.1-3          progress_1.2.2              httr_1.4.3                  GenomeInfoDb_1.32.2        
 [9] tools_4.2.1                 utf8_1.2.2                  R6_2.5.1                    KernSmooth_2.23-20         
[13] DBI_1.1.3                   BiocGenerics_0.42.0         colorspace_2.0-3            tidyselect_1.1.2           
[17] prettyunits_1.1.1           DESeq2_1.36.0               bit_4.0.4                   curl_4.3.2                 
[21] compiler_4.2.1              cli_3.3.0                   Biobase_2.56.0              xml2_1.3.3                 
[25] DelayedArray_0.22.0         rtracklayer_1.56.1          caTools_1.18.2              scales_1.2.0               
[29] genefilter_1.78.0           rappdirs_0.3.3              stringr_1.4.0               digest_0.6.29              
[33] Rsamtools_2.12.0            XVector_0.36.0              pkgconfig_2.0.3             MatrixGenerics_1.8.1       
[37] dbplyr_2.2.1                fastmap_1.1.0               rlang_1.0.4                 rstudioapi_0.13            
[41] RSQLite_2.2.14              BiocIO_1.6.0                generics_0.1.3              gtools_3.9.3               
[45] BiocParallel_1.30.3         dplyr_1.0.9                 RCurl_1.98-1.7              magrittr_2.0.3             
[49] GenomeInfoDbData_1.2.8      Matrix_1.4-1                Rcpp_1.0.9                  munsell_0.5.0              
[53] S4Vectors_0.34.0            fansi_1.0.3                 lifecycle_1.0.1             stringi_1.7.8              
[57] yaml_2.3.5                  SummarizedExperiment_1.26.1 zlibbioc_1.42.0             gplots_3.1.3               
[61] BiocFileCache_2.4.0         grid_4.2.1                  blob_1.2.3                  parallel_4.2.1             
[65] crayon_1.5.1                lattice_0.20-45             Biostrings_2.64.0           splines_4.2.1              
[69] GenomicFeatures_1.48.3      annotate_1.74.0             hms_1.1.1                   KEGGREST_1.36.3            
[73] locfit_1.5-9.6              pillar_1.8.0                GenomicRanges_1.48.0        rjson_0.2.21               
[77] geneplotter_1.74.0          codetools_0.2-18            biomaRt_2.52.0              stats4_4.2.1               
[81] XML_3.99-0.10               glue_1.6.2                  data.table_1.14.2           png_0.1-7                  
[85] vctrs_0.4.1                 gtable_0.3.0                purrr_0.3.4                 assertthat_0.2.1           
[89] cachem_1.0.6                ggplot2_3.3.6               xtable_1.8-4                restfulr_0.0.15            
[93] survival_3.3-1              tibble_3.1.7                GenomicAlignments_1.32.0    AnnotationDbi_1.58.0       
[97] memoise_2.0.1               IRanges_2.30.0              ellipsis_0.3.2             
>