error in kimono function
Closed this issue · 6 comments
when using kimono function it gives the error
Error in infer_network(input_data, prior_network, imputed_data, method, :
object '..data_filter' not found
How to resolve this?
Hi!
Could you please provide a script snippet of the code used and the output from "sessionInfo()" to get a better idea of the origin of the error?
Thanks in advance
Sure
I have attached script snippet of the code and output for sessionInfo() is given below:
R version 4.3.2 (2023-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22631)
Matrix products: default
locale:
[1] LC_COLLATE=English_India.utf8 LC_CTYPE=English_India.utf8 LC_MONETARY=English_India.utf8
[4] LC_NUMERIC=C LC_TIME=English_India.utf8
time zone: Asia/Calcutta
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] DT_0.32 cowplot_1.1.3 kimono_2.0.1.0006 hmlasso_0.0.1 checkmate_2.3.1
[6] miselect_0.9.2 impute_1.76.0 mice_3.16.0 lubridate_1.9.3 forcats_1.0.0
[11] stringr_1.5.1 purrr_1.0.2 readr_2.1.5 tidyr_1.3.1 tibble_3.2.1
[16] ggplot2_3.5.0 tidyverse_2.0.0 doSNOW_1.0.20 snow_0.4-4 iterators_1.0.14
[21] igraph_2.0.2 foreach_1.5.2 oem_2.0.11 bigmemory_4.6.4 dplyr_1.1.4
[26] data.table_1.15.0
loaded via a namespace (and not attached):
[1] gtable_0.3.4 shape_1.4.6.1 htmlwidgets_1.6.4 lattice_0.22-5
[5] tzdb_0.4.0 vctrs_0.6.5 tools_4.3.2 generics_0.1.3
[9] parallel_4.3.2 fansi_1.0.6 pan_1.9 pkgconfig_2.0.3
[13] jomo_2.7-6 Matrix_1.6-5 uuid_1.2-0 lifecycle_1.0.4
[17] compiler_4.3.2 munsell_0.5.0 codetools_0.2-19 htmltools_0.5.7
[21] glmnet_4.1-8 pillar_1.9.0 nloptr_2.0.3 MASS_7.3-60.0.1
[25] rpart_4.1.23 boot_1.3-29 mitml_0.4-5 RSpectra_0.16-1
[29] nlme_3.1-164 digest_0.6.34 tidyselect_1.2.0 stringi_1.8.3
[33] splines_4.3.2 fastmap_1.1.1 grid_4.3.2 colorspace_2.1-0
[37] cli_3.6.2 magrittr_2.0.3 survival_3.5-8 utf8_1.2.4
[41] broom_1.0.5 bigmemory.sri_0.1.8 withr_3.0.0 scales_1.3.0
[45] backports_1.4.1 timechange_0.3.0 nnet_7.3-19 lme4_1.1-35.1
[49] hms_1.1.3 rlang_1.1.3 Rcpp_1.0.12 glue_1.7.0
[53] rstudioapi_0.15.0 minqa_1.2.6 R6_2.5.1
Kimono.zip
Hi!
Thanks for your quick response!
The origin of the error could be caused by a mismatch between node names in the prior network and column names in the expression tables.
Please check if that is the source of the error.
You can check as well the following line data_filter <- colnames(input_data[[i]]) %in% node_names, where i is a layer in your input_data, e.g. gene or protein.
Kind regards,
Juan
Thank you for your suggestion but even after matching the node names in the prior network and the column names I am still facing the same issue.
Hi!
I was checking you script. I assume the list of omics matrices you are using are data frames. If so, please convert them into data tables.
Otherwise, please let me know to check if I can detect other sources triggering the error.
Kind regards,
Juan
The issue was resolved after converting into data tables.
Thank you so much for your help.
Regards,
Vamika Karn