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.
(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.)
1. Bug description
Unable to find an inherited method for function 'mcols' when running EpiCompare() function with CUT&Tag data peak files.
Console output
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)
(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.)
Data
KCZ0346_mus_CR018_PU1_CUTTag_H3K27ac_diagenode_20221122_R1.macs2_peaks.xls
3. Session info
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