error: no slot of name "options" for this object of class "infercnv"

[AlexanderAivazidis]

Hello,

From the issues I read about this it could be due to having an old version of the package, but I checked and I think I have the newest version: infercnv_1.3.6 I also attach my sessionInfo at the very bottom.

To reproduce the error I attach the 'glioblastoma_counts_subset.txt' and 'sample_annotation_subset.txt' file. Furtheremore, I used the gene_order_file from here: https://data.broadinstitute.org/Trinity/CTAT/cnv/gencode_v19_gene_pos.txt

This works fine:

inferncv_obj = CreateInfercnvObject(raw_counts_matrix="glioblastoma_counts_subset.txt", annotations_file="sample_annotation_subset.txt", delim = "\t", gene_order_file = "gencode_v19_gene_pos.txt", ref_group_names = NULL) INFO [2020-04-26 15:25:14] Parsing matrix: glioblastoma_counts_subset.txt INFO [2020-04-26 15:25:14] Parsing gene order file: gencode_v19_gene_pos.txt INFO [2020-04-26 15:25:14] Parsing cell annotations file: sample_annotation_subset.txt INFO [2020-04-26 15:25:14] ::order_reduce:Start. INFO [2020-04-26 15:25:14] .order_reduce(): expr and order match. INFO [2020-04-26 15:25:14] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 21673,10 Total=316614 Min=0 Max=1154. INFO [2020-04-26 15:25:14] num genes removed taking into account provided gene ordering list: 946 = 4.36487795875052% removed. INFO [2020-04-26 15:25:14] validating infercnv_obj

But here comes an error:

infercnv_obj = run(infercnv_obj,

• cutoff=0.1, # use 1 for smart-seq, 0.1 for 10x-genomics
• out_dir="/home/jovyan/HB_ZIK/inferCNV", # dir is auto-created for storing outputs
• cluster_by_groups=T, # cluster
• denoise=T,
• HMM=T
• )# INFO [2020-04-26 15:26:27] ::process_data:Start Error in run(infercnv_obj, cutoff = 0.1, out_dir = "/home/jovyan/HB_ZIK/inferCNV", : no slot of name "options" for this object of class "infercnv"

Here is my session info:

sessionInfo() R Under development (unstable) (2020-01-28 r77738) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 10 (buster)

Matrix products: default BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.3.5.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=C
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] NGCHM_0.12.2 infercnvNGCHM_0.1.0 infercnv_1.3.6
[4] BiocManager_1.30.10

loaded via a namespace (and not attached): [1] nlme_3.1-145 fs_1.3.2
[3] bitops_1.0-6 matrixStats_0.56.0
[5] usethis_1.5.1 devtools_2.2.2
[7] httr_1.4.1 doParallel_1.0.15
[9] RColorBrewer_1.1-2 rprojroot_1.3-2
[11] GenomeInfoDb_1.23.17 backports_1.1.6
[13] tools_4.0.0 R6_2.4.1
[15] KernSmooth_2.23-16 BiocGenerics_0.33.3
[17] colorspace_1.4-1 withr_2.2.0
[19] npsurv_0.4-0 tidyselect_1.0.0
[21] gridExtra_2.3 prettyunits_1.1.1
[23] processx_3.4.2 curl_4.3
[25] compiler_4.0.0 cli_2.0.2
[27] argparse_2.0.1 Biobase_2.47.3
[29] formatR_1.7 desc_1.2.0
[31] DelayedArray_0.13.12 sandwich_2.5-1
[33] caTools_1.18.0 scales_1.1.0
[35] mvtnorm_1.1-0 callr_3.4.3
[37] digest_0.6.25 XVector_0.27.2
[39] pkgconfig_2.0.3 sessioninfo_1.1.1
[41] limma_3.43.8 rlang_0.4.5
[43] zoo_1.8-7 jsonlite_1.6.1
[45] gtools_3.8.2 dplyr_0.8.5
[47] RCurl_1.98-1.2 magrittr_1.5
[49] modeltools_0.2-23 GenomeInfoDbData_1.2.3
[51] futile.logger_1.4.3 Matrix_1.2-18
[53] Rcpp_1.0.4.6 munsell_0.5.0
[55] S4Vectors_0.25.15 fansi_0.4.1
[57] ape_5.3 lifecycle_0.2.0
[59] multcomp_1.4-13 edgeR_3.29.1
[61] MASS_7.3-51.5 SummarizedExperiment_1.17.5 [63] zlibbioc_1.33.1 pkgbuild_1.0.7
[65] gplots_3.0.3 plyr_1.8.6
[67] grid_4.0.0 parallel_4.0.0
[69] gdata_2.18.0 listenv_0.8.0
[71] crayon_1.3.4 lattice_0.20-40
[73] splines_4.0.0 findpython_1.0.5
[75] locfit_1.5-9.4 ps_1.3.2
[77] pillar_1.4.3 fastcluster_1.1.25
[79] GenomicRanges_1.39.3 pkgload_1.0.2
[81] codetools_0.2-16 stats4_4.0.0
[83] futile.options_1.0.1 glue_1.4.0
[85] lsei_1.2-0 remotes_2.1.1
[87] lambda.r_1.2.4 vctrs_0.2.4
[89] foreach_1.5.0 testthat_2.3.2
[91] gtable_0.3.0 purrr_0.3.4
[93] tidyr_1.0.2 reshape_0.8.8
[95] future_1.17.0 assertthat_0.2.1
[97] ggplot2_3.3.0 coin_1.3-1
[99] libcoin_1.0-5 coda_0.19-3
[101] survival_3.1-11 rjags_4-10
[103] tsvio_0.0.13.9004 SingleCellExperiment_1.9.3 [105] tibble_3.0.1 iterators_1.0.12
[107] memoise_1.1.0 IRanges_2.21.8
[109] globals_0.12.5 fitdistrplus_1.0-14
[111] TH.data_1.0-10 ellipsis_0.3.0

Thanks for your help!

Alexander

sample_annotation_subset.txt glioblastoma_counts_subset.txt

[GeorgescuC]

Hi @AlexanderAivazidis ,

Is your output folder out_dir="/home/jovyan/HB_ZIK/inferCNV" empty? The issue can happen if you have objects generated with an older version of infercnv that it tries to reload. If that is the case, you can either empty the folder or use the resume_mode=FALSE option to avoid reloading.

Regards, Christophe.

[AlexanderAivazidis]

Hi Christophe,

thanks for getting back to me! But yes the folder is empty...

Best wishes,

Alexander

[GeorgescuC]

Hi @AlexanderAivazidis ,

Looking again at your code, it looks like there is a typo in the first command you run, which generates an object called inferncv_obj rather than infercnv_obj. Later when you call run() on infercnv_obj, it does not find it in your workspace and loads it from the package example files (that can be sourced with data() ) which were generated using an older version. I will be updating those files and changing the names to make it less likely that they are imported without realizing it.

Regards, Christophe.

[AlexanderAivazidis]

You are right that was it! Sorry about that... And thanks for helping! Best wishes, Alexander