Function overlap_percent report error unused arguments (peaklist1 = peaks, peaklist2 = reference_peak)

Xindong-Sun commented 2 years ago

1. Bug description

I am trying to get the overlap array by using the EpiCompare function overlap_percent, where I type overlap <- overlap_percent(peaklist1=peaks, peaklist2=reference_peak) according to the guidance above and an error was reported as, unused arguments (peaklist1 = peaks, peaklist2 = reference_peak).

Console output

Error in EpiCompare::overlap_percent(peaklist1 = CnT_H3K27ac, peaklist2 = encode_H3K27ac) : 
  unused arguments (peaklist1 = CnT_H3K27ac, peaklist2 = encode_H3K27ac)

Expected behaviour

Get the pairwise peak overlap array.

2. Reproducible example

Code

(Please add the steps to reproduce the bug here. See here for an intro to making a reproducible example (i.e. reprex) and why they're important! This will help us to help you much faster.)

library(EpiCompare)
data("encode_H3K27ac") # example peakfile GRanges object
data("CnT_H3K27ac") # example peakfile GRanges object
data("CnR_H3K27ac") # example peakfile GRanges object
#' ### Create Named Peaklist ###
peaks <- list("CnT"=CnT_H3K27ac, "CnR"=CnR_H3K27ac)
reference_peak <- list("ENCODE"=encode_H3K27ac)
overlap <- EpiCompare::overlap_percent(peaklist1=CnT_H3K27ac,
                peaklist2=encode_H3K27ac)

Data

(If possible, upload a small sample of your data so that we can reproduce the bug on our end. If that's not possible, please at least include a screenshot of your data and other relevant details.)

3. Session info

(Add output of the R function utils::sessionInfo() below. This helps us assess version/OS conflicts which could be causing bugs.)

``` R version 4.2.1 (2022-06-23) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Monterey 12.5 Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] EpiCompare_1.0.0 GenomicRanges_1.48.0 GenomeInfoDb_1.32.2 IRanges_2.30.0 [5] S4Vectors_0.34.0 BiocGenerics_0.42.0 loaded via a namespace (and not attached): [1] utf8_1.2.2 tidyselect_1.1.2 [3] htmlwidgets_1.5.4 RSQLite_2.2.14 [5] AnnotationDbi_1.58.0 grid_4.2.1 [7] BiocParallel_1.30.3 scatterpie_0.1.7 [9] munsell_0.5.0 codetools_0.2-18 [11] colorspace_2.0-3 GOSemSim_2.22.0 [13] Biobase_2.56.0 filelock_1.0.2 [15] knitr_1.39 rstudioapi_0.13 [17] DOSE_3.22.0 MatrixGenerics_1.8.1 [19] GenomeInfoDbData_1.2.8 polyclip_1.10-0 [21] seqPattern_1.28.0 bit64_4.0.5 [23] farver_2.1.1 downloader_0.4 [25] vctrs_0.4.1 treeio_1.20.0 [27] generics_0.1.3 xfun_0.31 [29] BiocFileCache_2.4.0 R6_2.5.1 [31] graphlayouts_0.8.0 locfit_1.5-9.6 [33] bitops_1.0-7 BRGenomics_1.8.0 [35] cachem_1.0.6 fgsea_1.22.0 [37] gridGraphics_0.5-1 DelayedArray_0.22.0 [39] assertthat_0.2.1 promises_1.2.0.1 [41] BiocIO_1.6.0 scales_1.2.0 [43] ggraph_2.0.5 enrichplot_1.16.1 [45] gtable_0.3.0 tidygraph_1.2.1 [47] rlang_1.0.4 genefilter_1.78.0 [49] splines_4.2.1 rtracklayer_1.56.1 [51] lazyeval_0.2.2 impute_1.70.0 [53] plyranges_1.16.0 BiocManager_1.30.18 [55] yaml_2.3.5 reshape2_1.4.4 [57] GenomicFeatures_1.48.3 httpuv_1.6.5 [59] qvalue_2.28.0 clusterProfiler_4.4.4 [61] tools_4.2.1 ggplotify_0.1.0 [63] gridBase_0.4-7 ggplot2_3.3.6 [65] ellipsis_0.3.2 gplots_3.1.3 [67] RColorBrewer_1.1-3 Rcpp_1.0.9 [69] plyr_1.8.7 progress_1.2.2 [71] zlibbioc_1.42.0 purrr_0.3.4 [73] RCurl_1.98-1.7 prettyunits_1.1.1 [75] viridis_0.6.2 SummarizedExperiment_1.26.1 [77] ggrepel_0.9.1 magrittr_2.0.3 [79] data.table_1.14.2 DO.db_2.9 [81] matrixStats_0.62.0 evaluate_0.15 [83] hms_1.1.1 patchwork_1.1.1 [85] mime_0.12 xtable_1.8-4 [87] XML_3.99-0.10 gridExtra_2.3 [89] compiler_4.2.1 biomaRt_2.52.0 [91] tibble_3.1.7 KernSmooth_2.23-20 [93] crayon_1.5.1 shadowtext_0.1.2 [95] htmltools_0.5.2 ggfun_0.0.6 [97] later_1.3.0 tzdb_0.3.0 [99] tidyr_1.2.0 geneplotter_1.74.0 [101] aplot_0.1.6 DBI_1.1.3 [103] tweenr_1.0.2 ChIPseeker_1.32.0 [105] genomation_1.28.0 dbplyr_2.2.1 [107] MASS_7.3-57 rappdirs_0.3.3 [109] boot_1.3-28 Matrix_1.4-1 [111] readr_2.1.2 cli_3.3.0 [113] parallel_4.2.1 igraph_1.3.2 [115] pkgconfig_2.0.3 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 [117] GenomicAlignments_1.32.0 plotly_4.10.0 [119] xml2_1.3.3 ggtree_3.4.0 [121] annotate_1.74.0 XVector_0.36.0 [123] yulab.utils_0.0.5 stringr_1.4.0 [125] digest_0.6.29 Biostrings_2.64.0 [127] rmarkdown_2.14 fastmatch_1.1-3 [129] tidytree_0.3.9 restfulr_0.0.15 [131] curl_4.3.2 shiny_1.7.1 [133] Rsamtools_2.12.0 gtools_3.9.3 [135] rjson_0.2.21 lifecycle_1.0.1 [137] nlme_3.1-158 jsonlite_1.8.0 [139] viridisLite_0.4.0 BSgenome_1.64.0 [141] fansi_1.0.3 pillar_1.7.0 [143] lattice_0.20-45 KEGGREST_1.36.2 [145] fastmap_1.1.0 httr_1.4.3 [147] plotrix_3.8-2 survival_3.3-1 [149] GO.db_3.15.0 interactiveDisplayBase_1.34.0 [151] glue_1.6.2 UpSetR_1.4.0 [153] png_0.1-7 BiocVersion_3.15.2 [155] bit_4.0.4 ggforce_0.3.3 [157] stringi_1.7.8 blob_1.2.3 [159] DESeq2_1.36.0 org.Hs.eg.db_3.15.0 [161] AnnotationHub_3.4.0 caTools_1.18.2 [163] memoise_2.0.1 dplyr_1.0.9 [165] ape_5.6-2 ```

bschilder commented 2 years ago

@serachoi1230 I think this might be due to a disconnect between the dev version v0.99.21 (and its documentation on GitHub Pages), and the Bioc release version v1.0.0 (which @Xindong-ZJU is using). I also noticed that the Bioc devel version is v1.1.0, which does not match up with the version on GitHub. @serachoi1230 can you update the version number in the DESCRIPTION to 1.1.1 and push an update to Bioc devel?

@Xindong-ZJU could you try installing the dev version from GitHub and retrying?

remotes::install_github("neurogenomics/EpiCompare")

Xindong-Sun commented 2 years ago

Thanks Brian! It works now :) 👍

neurogenomics / EpiCompare