friedue / rmagic Goto Github PK

The %^% function is absent but there is a cryptic 'stub' for this function in https://github.com/friedue/Rmagic/blob/master/man/grapes-pow-grapes.Rd

Also in the Markov normalization, this line fails
W <- W/rowSums(W)

but this works:
W <- W/rowSums(as.matrix(W)) since W is a sparse matrix

sessionInfo()

R version 3.4.1 (2017-06-30)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

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

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

other attached packages:
[1] gplots_3.0.1 RColorBrewer_1.1-2 FNN_1.1 rsvd_0.6 Rmagic_0.1.0
[7] dplyr_0.7.4 Seurat_2.1.0 synchronicity_1.1.9.1 bigmemory_4.5.28 bigmemory.sri_0.1.3 Biobase_2.38.0
[13] BiocGenerics_0.24.0 Matrix_1.2-11 cowplot_0.9.1 ggplot2_2.2.1

loaded via a namespace (and not attached):
[1] diffusionMap_1.1-0 Rtsne_0.13 VGAM_1.0-4 colorspace_1.3-2 ggridges_0.4.1 class_7.3-14
[7] modeltools_0.2-21 mclust_5.3 htmlTable_1.9 base64enc_0.1-3 proxy_0.4-19 DRR_0.0.2
[13] flexmix_2.3-13 prodlim_1.6.1 mvtnorm_1.0-6 lubridate_1.7.1 ranger_0.8.0 codetools_0.2-15
[19] splines_3.4.1 R.methodsS3_1.7.1 mnormt_1.5-5 doParallel_1.0.11 robustbase_0.92-8 knitr_1.17
[25] tclust_1.3-1 RcppRoll_0.2.2 Formula_1.2-2 caret_6.0-77 ica_1.0-1 gridBase_0.4-7
[31] ddalpha_1.3.1 cluster_2.0.6 kernlab_0.9-25 R.oo_1.21.0 sfsmisc_1.1-1 compiler_3.4.1
[37] backports_1.1.1 assertthat_0.2.0 lazyeval_0.2.1 lars_1.2 acepack_1.4.1 htmltools_0.3.6
[43] tools_3.4.1 bindrcpp_0.2 igraph_1.1.2 gtable_0.2.0 glue_1.2.0 reshape2_1.4.2
[49] Rcpp_0.12.13 NMF_0.20.6 trimcluster_0.1-2 gdata_2.18.0 ape_5.0 nlme_3.1-131
[55] iterators_1.0.8 fpc_2.1-10 timeDate_3042.101 gower_0.1.2 stringr_1.2.0 irlba_2.3.1
[61] rngtools_1.2.4 gtools_3.5.0 DEoptimR_1.0-8 MASS_7.3-47 scales_0.5.0 ipred_0.9-6
[67] pbapply_1.3-3 gridExtra_2.3 pkgmaker_0.22 segmented_0.5-2.2 rpart_4.1-11 latticeExtra_0.6-28
[73] stringi_1.1.6 foreach_1.4.3 checkmate_1.8.5 caTools_1.17.1 ggjoy_0.4.0 lava_1.5.1
[79] dtw_1.18-1 SDMTools_1.1-221 rlang_0.1.4 pkgconfig_2.0.1 prabclus_2.2-6 bitops_1.0-6
[85] lattice_0.20-35 ROCR_1.0-7 purrr_0.2.4 bindr_0.1 labeling_0.3 recipes_0.1.0
[91] htmlwidgets_0.9 CVST_0.2-1 plyr_1.8.4 R6_2.2.2 Hmisc_4.0-3 dimRed_0.1.0
[97] sn_1.5-0 foreign_0.8-69 withr_2.1.0 mixtools_1.1.0 survival_2.41-3 scatterplot3d_0.3-40
[103] nnet_7.3-12 tsne_0.1-3 tibble_1.3.4 KernSmooth_2.23-15 grid_3.4.1 data.table_1.10.4-3
[109] ModelMetrics_1.1.0 digest_0.6.12 diptest_0.75-7 xtable_1.8-2 tidyr_0.7.2 numDeriv_2016.8-1
[115] R.utils_2.6.0 stats4_3.4.1 munsell_0.4.3 registry_0.3