Tutorial doesn't work - Githubissues

ajandria commented 1 year ago

Hello @Jiaxin-Fan,

I need help with the error your tutorial is giving me

> # music2 deconvolution
> set.seed(1234)
> est.prop = music2_prop(
+   bulk.eset = benchmark.eset,
+   sc.eset = seger.eset,
+   condition = 'group',
+   control = 'healthy',
+   case = 't2d',
+   clusters = 'cellType',
+   samples = 'sampleID',
+   select.ct = c('acinar', 'alpha', 'beta', 'delta', 'ductal', 'gamma'),
+   n_resample = 20,
+   sample_prop = 0.5,
+   cutoff_c = 0.05,
+   cutoff_r = 0.01
+ )$Est.prop
Error in rownames(bulk.mtx) : 
  argument "bulk.mtx" is missing, with no default

xoelmb commented 1 year ago

I have just installed MuSiC2 and I am encountering this same error.

R version 4.2.1 (2022-06-23) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Ubuntu 20.04.5 LTS

Matrix products: default BLAS/LAPACK: /users/genomics/xoel/micromamba/envs/music2/lib/libopenblasp-r0.3.21.so

locale: [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] MuSiC2_0.1.0 Biobase_2.56.0 BiocGenerics_0.42.0

loaded via a namespace (and not attached): [1] mcmc_0.9-7 bitops_1.0-7
[3] matrixStats_0.62.0 MuSiC_1.0.0
[5] bit64_4.0.5 httr_1.4.4
[7] doParallel_1.0.17 RColorBrewer_1.1-3
[9] GenomeInfoDb_1.32.4 repr_1.1.4
[11] backports_1.4.1 tools_4.2.1
[13] utf8_1.2.2 R6_2.5.1
[15] DBI_1.1.3 colorspace_2.0-3
[17] withr_2.5.0 tidyselect_1.2.0
[19] GGally_2.1.2 xbioc_0.1.19
[21] bit_4.0.4 compiler_4.2.1
[23] cli_3.4.1 quantreg_5.94
[25] SparseM_1.81 pkgmaker_0.32.2.900
[27] DelayedArray_0.22.0 checkmate_2.1.0
[29] scales_1.2.1 nnls_1.4
[31] quadprog_1.5-8 proxy_0.4-27
[33] pbdZMQ_0.3-7 stringr_1.4.1
[35] digest_0.6.30 MCMCpack_1.6-3
[37] XVector_0.36.0 base64enc_0.1-3
[39] pkgconfig_2.0.3 htmltools_0.5.3
[41] MatrixGenerics_1.8.1 fastmap_1.1.0
[43] limma_3.52.4 rlang_1.0.6
[45] RSQLite_2.2.18 generics_0.1.3
[47] jsonlite_1.8.2 dplyr_1.0.10
[49] RCurl_1.98-1.9 magrittr_2.0.3
[51] GenomeInfoDbData_1.2.8 Matrix_1.5-1
[53] Rcpp_1.0.9 IRkernel_1.3
[55] munsell_0.5.0 S4Vectors_0.34.0
[57] fansi_1.0.3 lifecycle_1.0.3
[59] stringi_1.7.8 MASS_7.3-58.1
[61] SummarizedExperiment_1.26.1 zlibbioc_1.42.0
[63] plyr_1.8.7 grid_4.2.1
[65] blob_1.2.3 parallel_4.2.1
[67] crayon_1.5.2 lattice_0.20-45
[69] Biostrings_2.64.1 IRdisplay_1.1
[71] splines_4.2.1 KEGGREST_1.36.3
[73] pillar_1.8.1 GenomicRanges_1.48.0
[75] uuid_1.1-0 corpcor_1.6.10
[77] reshape2_1.4.4 codetools_0.2-18
[79] stats4_4.2.1 glue_1.6.2
[81] evaluate_0.17 EpiDISH_2.12.0
[83] BiocManager_1.30.18 png_0.1-7
[85] vctrs_0.4.2 foreach_1.5.2
[87] locfdr_1.1-8 MatrixModels_0.5-1
[89] gtable_0.3.1 purrr_0.3.5
[91] tidyr_1.2.1 reshape_0.8.9
[93] assertthat_0.2.1 cachem_1.0.6
[95] ggplot2_3.3.6 TOAST_1.10.1
[97] xtable_1.8-4 e1071_1.7-11
[99] coda_0.19-4 class_7.3-20
[101] survival_3.4-0 tibble_3.1.8
[103] iterators_1.0.14 registry_0.5-1
[105] AnnotationDbi_1.58.0 memoise_2.0.1
[107] IRanges_2.30.1