EpiCompare Function Error - Unable to find an inherited method for function 'mcols'

[ParisaRahbar]

1. Bug description

Unable to find an inherited method for function 'mcols' when running EpiCompare() function with CUT&Tag data peak files.

Console output

 Quitting from lines 55-111 (EpiCompare.Rmd) 
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'mcols' for signature '"character"'

Expected behaviour

I have tried updating all my packages, including Bioconductor, and even tested the function with an example input data, but the error persists. EpiCompare() function should run without any errors, allowing comparative analysis of the peak files.

2. Reproducible example

library(EpiCompare)

TF1_pu1_mm10_path <- "/Volumes/pr422/projects/epinott/live/Nextflow/cut_tag/analysed_data/ADvas_PRR_20230405_p1/03_peak_calling/04_called_peaks/macs2/KCZ0342_mus_CR018_PU1_CUTTag_rIgG_linear_20221122_R1.macs2.peaks.cut.bed"
His_pu1_mm10_path <- "/Volumes/pr422/projects/epinott/live/Nextflow/cut_tag/analysed_data/ADvas_PRR_20230405_p1/03_peak_calling/04_called_peaks/macs2/KCZ0346_mus_CR018_PU1_CUTTag_H3K27ac_diagenode_20221122_R1.macs2.peaks.cut.bed"
TF1_pu1_mm10 <- import(TF1_pu1_mm10_path)
His_pu1_mm10 <- import(His_pu1_mm10_path)
peakfiles <- list("TF1_pu1_mm10" = TF1_pu1_mm10,

•               "His_pu1_mm10" = His_pu1_mm10)
  

comparing <- EpiCompare(peakfiles = peakfiles,

•                     genome_build = "mm10", genome_build_output = "hg19", blacklist = "mm10_blacklist", output_dir = "/Volumes/pr422/projects/epinott/live/user_analysed_data/Parisa/",
  

•                     save_output = TRUE)
  

(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.)

# Paste example here

Data

KCZ0346_mus_CR018_PU1_CUTTag_H3K27ac_diagenode_20221122_R1.macs2_peaks.xls

3. Session info

utils::sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.3

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/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] stats4 stats graphics grDevices utils datasets methods base

other attached packages:
[1] rtracklayer_1.58.0 GenomicRanges_1.50.2 GenomeInfoDb_1.34.9 IRanges_2.32.0
[5] S4Vectors_0.36.2 BiocGenerics_0.44.0 EpiCompare_1.2.0

loaded via a namespace (and not attached):
[1] genomation_1.30.0 shadowtext_0.1.2
[3] ChIPseeker_1.34.1 AnnotationHub_3.6.0
[5] fastmatch_1.1-3 BiocFileCache_2.6.1
[7] plyr_1.8.8 igraph_1.4.2
[9] lazyeval_0.2.2 splines_4.2.2
[11] BiocParallel_1.32.6 gridBase_0.4-7
[13] ggplot2_3.4.2 digest_0.6.31
[15] yulab.utils_0.0.6 htmltools_0.5.5
[17] GOSemSim_2.24.0 viridis_0.6.2
[19] GO.db_3.16.0 fansi_1.0.4
[21] magrittr_2.0.3 memoise_2.0.1
[23] BSgenome_1.66.3 tzdb_0.3.0
[25] readr_2.1.4 Biostrings_2.66.0
[27] annotate_1.76.0 graphlayouts_0.8.4
[29] matrixStats_0.63.0 enrichplot_1.18.4
[31] prettyunits_1.1.1 colorspace_2.1-0
[33] blob_1.2.4 rappdirs_0.3.3
[35] ggrepel_0.9.3 xfun_0.39
[37] dplyr_1.1.2 jsonlite_1.8.4
[39] crayon_1.5.2 RCurl_1.98-1.12
[41] scatterpie_0.1.8 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[43] impute_1.72.3 ape_5.7-1
[45] glue_1.6.2 polyclip_1.10-4
[47] gtable_0.3.3 zlibbioc_1.44.0
[49] XVector_0.38.0 DelayedArray_0.24.0
[51] scales_1.2.1 DOSE_3.24.2
[53] DBI_1.1.3 Rcpp_1.0.10
[55] plotrix_3.8-2 viridisLite_0.4.1
[57] xtable_1.8-4 progress_1.2.2
[59] gridGraphics_0.5-1 tidytree_0.4.2
[61] bit_4.0.5 htmlwidgets_1.6.2
[63] httr_1.4.5 fgsea_1.24.0
[65] gplots_3.1.3 RColorBrewer_1.1-3
[67] ellipsis_0.3.2 pkgconfig_2.0.3
[69] XML_3.99-0.14 farver_2.1.1
[71] sass_0.4.5 dbplyr_2.3.2
[73] locfit_1.5-9.7 utf8_1.2.3
[75] ggplotify_0.1.0 tidyselect_1.2.0
[77] rlang_1.1.0 reshape2_1.4.4
[79] later_1.3.0 AnnotationDbi_1.60.2
[81] munsell_0.5.0 BiocVersion_3.16.0
[83] tools_4.2.2 cachem_1.0.7
[85] cli_3.6.1 generics_0.1.3
[87] RSQLite_2.3.1 evaluate_0.20
[89] stringr_1.5.0 BRGenomics_1.10.0
[91] fastmap_1.1.1 yaml_2.3.7
[93] ggtree_3.6.2 knitr_1.42
[95] bit64_4.0.5 tidygraph_1.2.3
[97] caTools_1.18.2 purrr_1.0.1
[99] KEGGREST_1.38.0 ggraph_2.1.0
[101] nlme_3.1-162 mime_0.12
[103] aplot_0.1.10 xml2_1.3.3
[105] biomaRt_2.54.1 compiler_4.2.2
[107] rstudioapi_0.14 plotly_4.10.1
[109] filelock_1.0.2 curl_5.0.0
[111] png_0.1-8 interactiveDisplayBase_1.36.0
[113] treeio_1.22.0 tibble_3.2.1
[115] tweenr_2.0.2 geneplotter_1.76.0
[117] bslib_0.4.2 stringi_1.7.12
[119] GenomicFeatures_1.50.4 lattice_0.21-8
[121] Matrix_1.5-4 vctrs_0.6.2
[123] pillar_1.9.0 lifecycle_1.0.3
[125] BiocManager_1.30.20 jquerylib_0.1.4
[127] data.table_1.14.8 cowplot_1.1.1
[129] bitops_1.0-7 httpuv_1.6.9
[131] patchwork_1.1.2 qvalue_2.30.0
[133] R6_2.5.1 BiocIO_1.8.0
[135] promises_1.2.0.1 KernSmooth_2.23-20
[137] gridExtra_2.3 codetools_0.2-19
[139] gtools_3.9.4 boot_1.3-28.1
[141] MASS_7.3-59 SummarizedExperiment_1.28.0
[143] DESeq2_1.38.3 rjson_0.2.21
[145] withr_2.5.0 GenomicAlignments_1.34.1
[147] Rsamtools_2.14.0 GenomeInfoDbData_1.2.9
[149] parallel_4.2.2 hms_1.1.3
[151] grid_4.2.2 ggfun_0.0.9
[153] tidyr_1.3.0 HDO.db_0.99.1
[155] rmarkdown_2.21 MatrixGenerics_1.10.0
[157] seqPattern_1.30.0 ggforce_0.4.1
[159] Biobase_2.58.0 shiny_1.7.4
[161] restfulr_0.0.15

# Paste utils::sessionInfo() output 

[bschilder]

Thanks for filling this out @ParisaRahbar .

@serachoi1230, when you have a chance would you mind looking into this?