A error message with "getNetwork" function

[zyb1984]

I tried to follow the tutorial from "https://bioconductor.org/packages/release/bioc/vignettes/BioTIP/inst/doc/BioTIP.html", but with an error message with "getNetwork" function, and the information is " error in getNetwork(testres, FDR = 0.2) : parameter is not used (FDR = 0.2) ". So, I tried to follow the simple example of "getNetwork" function like
"test = list('state1' = matrix(sample(1:10, 6), 2, 3),
'state2'=matrix(sample(1:10, 6), 2, 3),
'state3' = matrix(sample(1:10, 6), 2, 3))

for(i in names(test)){
colnames(test[[i]]) = 1:3
row.names(test[[i]]) = 1:2}

igraphL <- getNetwork(test, fdr=1)
#[1] "state1:2 nodes"
#[1] "state2:2 nodes"
#[1] "state3:2 nodes" "
Also with the same error "parameter isn't useful", and when I deleted the FDR parameters, and with another error "Error in getNetwork(testres) : Cannot get an "active" slot from an object of a base category ("list") that does not have slots "

sessionInfo()
R version 4.2.0 (2022-04-22 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8
[2] LC_CTYPE=Chinese (Simplified)_China.utf8
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.utf8

attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base

other attached packages:
[1] MASS_7.3-57 Hmisc_4.7-0
[3] Formula_1.2-4 survival_3.3-1
[5] lattice_0.20-45 LoomExperiment_1.14.0
[7] BiocIO_1.6.0 rhdf5_2.40.0
[9] zellkonverter_1.6.1 BiocManager_1.30.18
[11] DropletUtils_1.16.0 dplyr_1.0.9
[13] stxBrain.SeuratData_0.1.1 ssHippo.SeuratData_3.1.4
[15] pbmcsca.SeuratData_3.0.0 pbmc3k.SeuratData_3.1.4
[17] ifnb.SeuratData_3.1.0 hcabm40k.SeuratData_3.0.0
[19] bmcite.SeuratData_0.3.0 SeuratData_0.2.2
[21] RSCORE_0.1.0 org.Hs.eg.db_3.15.0
[23] clusterProfiler_4.4.1 genesorteR_0.4.3
[25] Matrix_1.4-1 doMC_1.3.5
[27] iterators_1.0.14 doRNG_1.8.2
[29] rngtools_1.5.2 foreach_1.5.2
[31] network_1.17.2 coop_0.6-3
[33] propr_4.2.6 STRINGdb_2.8.4
[35] AUCell_1.18.1 sp_1.4-7
[37] SeuratObject_4.1.0 Seurat_4.1.1
[39] BioTIP_1.10.0 stringr_1.4.0
[41] scran_1.24.0 scater_1.24.0
[43] ggplot2_3.3.6 scuttle_1.6.2
[45] psych_2.2.5 pheatmap_1.0.12
[47] org.Mm.eg.db_3.15.0 AnnotationDbi_1.58.0
[49] igraph_1.3.1 gridExtra_2.3
[51] gplots_3.1.3 edgeR_3.38.1
[53] limma_3.52.1 dynamicTreeCut_1.63-1
[55] corrplot_0.92 cluster_2.1.3
[57] batchelor_1.12.1 MouseGastrulationData_1.10.0
[59] SpatialExperiment_1.6.0 SingleCellExperiment_1.18.0
[61] SummarizedExperiment_1.26.1 Biobase_2.56.0
[63] GenomicRanges_1.48.0 GenomeInfoDb_1.32.2
[65] IRanges_2.30.0 S4Vectors_0.34.0
[67] BiocGenerics_0.42.0 MatrixGenerics_1.8.0
[69] matrixStats_0.62.0

loaded via a namespace (and not attached):
[1] statnet.common_4.6.0 rsvd_1.0.5
[3] ica_1.0-2 lmtest_0.9-40
[5] crayon_1.5.1 spatstat.core_2.4-4
[7] rhdf5filters_1.8.0 backports_1.4.1
[9] nlme_3.1-157 basilisk_1.8.0
[11] GOSemSim_2.22.0 rlang_1.0.2
[13] XVector_0.36.0 ROCR_1.0-11
[15] irlba_2.3.5 intergraph_2.0-2
[17] filelock_1.0.2 proto_1.0.0
[19] BiocParallel_1.30.2 rjson_0.2.21
[21] bit64_4.0.5 glue_1.6.2
[23] sctransform_0.3.3 vipor_0.4.5
[25] spatstat.sparse_2.1-1 DOSE_3.22.0
[27] spatstat.geom_2.4-0 tidyselect_1.1.2
[29] fitdistrplus_1.1-8 XML_3.99-0.9
[31] tidyr_1.2.0 zoo_1.8-10
[33] chron_2.3-57 xtable_1.8-4
[35] magrittr_2.0.3 cli_3.3.0
[37] zlibbioc_1.42.0 rstudioapi_0.13
[39] miniUI_0.1.1.1 rpart_4.1.16
[41] fastmatch_1.1-3 treeio_1.20.0
[43] shiny_1.7.1 xfun_0.31
[45] BiocSingular_1.12.0 caTools_1.18.2
[47] tidygraph_1.2.1 KEGGREST_1.36.0
[49] tibble_3.1.7 interactiveDisplayBase_1.34.0
[51] ggrepel_0.9.1 ape_5.6-2
[53] listenv_0.8.0 Biostrings_2.64.0
[55] png_0.1-7 permute_0.9-7
[57] future_1.26.1 withr_2.5.0
[59] bitops_1.0-7 ggforce_0.3.3
[61] plyr_1.8.7 GSEABase_1.58.0
[63] microeco_0.10.1 dqrng_0.3.0
[65] coda_0.19-4 pillar_1.7.0
[67] cachem_1.0.6 hash_2.2.6.2
[69] DelayedMatrixStats_1.18.0 vctrs_0.4.1
[71] ellipsis_0.3.2 generics_0.1.2
[73] gsubfn_0.7 tools_4.2.0
[75] foreign_0.8-82 beeswarm_0.4.0
[77] munsell_0.5.0 tweenr_1.0.2
[79] fgsea_1.22.0 DelayedArray_0.22.0
[81] fastmap_1.1.0 compiler_4.2.0
[83] abind_1.4-5 httpuv_1.6.5
[85] ExperimentHub_2.4.0 plotly_4.10.0
[87] rgeos_0.5-9 GenomeInfoDbData_1.2.8
[89] dir.expiry_1.4.0 deldir_1.0-6
[91] utf8_1.2.2 later_1.3.0
[93] BiocFileCache_2.4.0 jsonlite_1.8.0
[95] scales_1.2.0 graph_1.74.0
[97] ScaledMatrix_1.4.0 tidytree_0.3.9
[99] pbapply_1.5-0 sparseMatrixStats_1.8.0
[101] lazyeval_0.2.2 promises_1.2.0.1
[103] latticeExtra_0.6-29 R.utils_2.11.0
[105] goftest_1.2-3 checkmate_2.1.0
[107] spatstat.utils_2.3-1 reticulate_1.25
[109] cowplot_1.1.1 statmod_1.4.36
[111] Rtsne_0.16 downloader_0.4
[113] uwot_0.1.11 HDF5Array_1.24.1
[115] ResidualMatrix_1.6.0 yaml_2.3.5
[117] plotrix_3.8-2 htmltools_0.5.2
[119] memoise_2.0.1 locfit_1.5-9.5
[121] graphlayouts_0.8.0 viridisLite_0.4.0
[123] digest_0.6.29 assertthat_0.2.1
[125] mime_0.12 rappdirs_0.3.3
[127] RSQLite_2.2.14 sqldf_0.4-11
[129] yulab.utils_0.0.4 future.apply_1.9.0
[131] data.table_1.14.2 blob_1.2.3
[133] vegan_2.6-2 R.oo_1.24.0
[135] labeling_0.4.2 splines_4.2.0
[137] Rhdf5lib_1.18.2 AnnotationHub_3.4.0
[139] RCurl_1.98-1.6 base64enc_0.1-3
[141] colorspace_2.0-3 mnormt_2.0.2
[143] ggbeeswarm_0.6.0 tmvnsim_1.0-2
[145] aplot_0.1.6 nnet_7.3-17
[147] Rcpp_1.0.8.3 mclust_5.4.10
[149] RANN_2.6.1 enrichplot_1.16.1
[151] fansi_1.0.3 parallelly_1.31.1
[153] R6_2.5.1 grid_4.2.0
[155] ggridges_0.5.3 lifecycle_1.0.1
[157] bluster_1.6.0 curl_4.3.2
[159] leiden_0.4.2 DO.db_2.9
[161] qvalue_2.28.0 RcppAnnoy_0.0.19
[163] RColorBrewer_1.1-3 htmlwidgets_1.5.4
[165] beachmat_2.12.0 polyclip_1.10-0
[167] purrr_0.3.4 shadowtext_0.1.2
[169] gridGraphics_0.5-1 mgcv_1.8-40
[171] globals_0.15.0 BumpyMatrix_1.4.0
[173] htmlTable_2.4.0 patchwork_1.1.1
[175] spatstat.random_2.2-0 progressr_0.10.1
[177] codetools_0.2-18 FNN_1.1.3.1
[179] GO.db_3.15.0 metapod_1.4.0
[181] gtools_3.9.2.1 dbplyr_2.2.0
[183] RSpectra_0.16-1 basilisk.utils_1.8.0
[185] R.methodsS3_1.8.1 gtable_0.3.0
[187] DBI_1.1.2 ggfun_0.0.6
[189] tensor_1.5 httr_1.4.3
[191] KernSmooth_2.23-20 stringi_1.7.6
[193] reshape2_1.4.4 farver_2.1.0
[195] annotate_1.74.0 viridis_0.6.2
[197] ggtree_3.4.0 magick_2.7.3
[199] BiocNeighbors_1.14.0 ggplotify_0.1.0
[201] scattermore_0.8 BiocVersion_3.15.2
[203] bit_4.0.4 jpeg_0.1-9
[205] scatterpie_0.1.7 spatstat.data_2.2-0
[207] ggraph_2.0.5 pkgconfig_2.0.3
[209] knitr_1.39

[Ci-TJ]

@zyb1984
Hi! If I don't misunderstand your idea, maybe you misuse of upper and lower case. By the way, did you reproduce the scRNA-seq example in BioTIP's vignettes. Could you share me "cell_info.tsv"? I cannot generate it. My e-mail 1911449@tongji.edu.cn. Thank you!

library(BioTIP)
library(cluster)
library(GenomicRanges)
library(Hmisc)
library(MASS)
require(stringr)
require(psych)
require(igraph)
set.seed(123)
test = list('state1' = matrix(runif(3000, 1, 10), 300, 10),
            'state2' = matrix(runif(3000, 1, 10), 300, 10),
            'state3' = matrix(runif(3000, 1, 10), 300, 10),
            'state4' = matrix(runif(3000, 1, 10), 300, 10),
            'state5' = matrix(runif(3000, 1, 10), 300, 10))

for(i in names(test)){
    colnames(test[[i]]) = paste0("p",1:10)
    row.names(test[[i]]) = paste0("gene",1:300)}
igraphL <- getNetwork(test, fdr=1)
#> igraphL <- getNetwork(test, fdr=1)
#state1:300 nodes
#state2:300 nodes
#state3:300 nodes
#state4:300 nodes
#state5:300 nodes

##For Yours
set.seed(123)
test = list('state1' = matrix(sample(1:10, 6), 2, 3),
            'state2'=matrix(sample(1:10, 6), 2, 3),
            'state3' = matrix(sample(1:10, 6), 2, 3))

for(i in names(test)){
    colnames(test[[i]]) = 1:3
    row.names(test[[i]]) = 1:2}

igraphL <- getNetwork(test, fdr=1)
#> igraphL <- getNetwork(test, fdr=1)
#state1:2 nodes
#state2:2 nodes
#state3:2 nodes


##Maybe you misuse of upper and lower case
igraphL <- getNetwork(test, FDR=1)
#> igraphL <- getNetwork(test, FDR=1)
#Error in getNetwork(test, FDR = 1) : unused argument (FDR = 1)

> sessionInfo()
R version 4.2.0 (2022-04-22 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] igraph_1.3.1         psych_2.2.5          stringr_1.4.0       
 [4] MASS_7.3-57          Hmisc_4.7-0          ggplot2_3.3.6       
 [7] Formula_1.2-4        survival_3.3-1       lattice_0.20-45     
[10] GenomicRanges_1.48.0 GenomeInfoDb_1.32.2  IRanges_2.30.0      
[13] S4Vectors_0.34.0     BiocGenerics_0.42.0  cluster_2.1.3       
[16] BioTIP_1.10.0       

loaded via a namespace (and not attached):
 [1] png_0.1-7              digest_0.6.29          assertthat_0.2.1      
 [4] utf8_1.2.2             R6_2.5.1               backports_1.4.1       
 [7] pillar_1.7.0           zlibbioc_1.42.0        rlang_1.0.2           
[10] data.table_1.14.2      rstudioapi_0.13        rpart_4.1.16          
[13] Matrix_1.4-1           checkmate_2.1.0        splines_4.2.0         
[16] foreign_0.8-82         htmlwidgets_1.5.4      RCurl_1.98-1.6        
[19] munsell_0.5.0          xfun_0.31              compiler_4.2.0        
[22] pkgconfig_2.0.3        base64enc_0.1-3        mnormt_2.0.2          
[25] tmvnsim_1.0-2          htmltools_0.5.2        nnet_7.3-17           
[28] tidyselect_1.1.2       tibble_3.1.7           gridExtra_2.3         
[31] htmlTable_2.4.0        GenomeInfoDbData_1.2.8 fansi_1.0.3           
[34] crayon_1.5.1           dplyr_1.0.9            withr_2.5.0           
[37] bitops_1.0-7           grid_4.2.0             nlme_3.1-157          
[40] gtable_0.3.0           lifecycle_1.0.1        DBI_1.1.2             
[43] magrittr_2.0.3         scales_1.2.0           cli_3.3.0             
[46] stringi_1.7.6          XVector_0.36.0         latticeExtra_0.6-29   
[49] ellipsis_0.3.2         generics_0.1.2         vctrs_0.4.1           
[52] RColorBrewer_1.1-3     tools_4.2.0            glue_1.6.2            
[55] purrr_0.3.4            jpeg_0.1-9             fastmap_1.1.0         
[58] parallel_4.2.0         colorspace_2.0-3       knitr_1.39 

Best,
Qin

[zyb1984]

Thank you very much, all problems have been solved, and the new code works well.