jleechung
commented
2 years ago 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
>
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"