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athirak1986
•
0
@athirak1986-19127
Last seen 5.7 years ago
When I run the mgeneSim
function in the GOSemsim
package, choose ontology "BP" or "CC" or "MF" the error pop up as follows.
code:
library(GOSemSim) d <- godata('org.Sc.sgd.db', ont="BP", computeIC=TRUE) ORF_dat<-select(org.Sc.sgd.db, keys=k, keytype="ENTREZID", columns="ORF") ORF_vec<-as.character(ORF_dat$ORF) sim <- mgeneSim(ORF_vec,semData=d,measure="Wang",drop = NULL)
Result:
r in go_matrix[gos[[i]], gos[[j]]] : incorrect number of dimensions
when i run the following code
str(ORF_vec)
select(org.Sc.sgd.db, keys=ORF_vec, keytype="ORF", "GO")
got the result
chr [1:20] "YMR084W" "YFL026W" "YPL228W" "YDR110W" "YPL081W" "YDR204W" "YAR009C" "YHR167W" "YLR390W-A" "YLR421C" "YPR089W" ...
1 YMR084W S000004689 GO:0003674 ND MF 2 YMR084W S000004689 GO:0004360 IEA MF 3 YMR084W S000004689 GO:0005575 ND CC 4 YMR084W S000004689 GO:0006048 IEA BP 5 YMR084W S000004689 GO:0006541 IEA BP 6 YMR084W S000004689 GO:0008150 ND BP 7 YMR084W S000004689 GO:0008483 IEA MF 8 YMR084W S000004689 GO:0016740 IEA MF 9 YFL026W S000001868 GO:0000750 IMP BP 10 YFL026W S000001868 GO:0000755 IDA BP 11 YFL026W S000001868 GO:0000755 IMP BP 12 YFL026W S000001868 GO:0004871 IEA MF 13 YFL026W S000001868 GO:0004930 IEA MF 14 YFL026W S000001868 GO:0004932 IEA MF 15 YFL026W S000001868 GO:0004934 IDA MF 16 YFL026W S000001868 GO:0004934 IGI MF 17 YFL026W S000001868 GO:0004934 IMP MF 18 YFL026W S000001868 GO:0004934 ISS MF 19 YFL026W S000001868 GO:0005550 IBA MF 20 YFL026W S000001868 GO:0005887 IDA CC 21 YFL026W S000001868 GO:0007165 IEA BP 22 YFL026W S000001868 GO:0007186 IEA BP 23 YFL026W S000001868 GO:0016020 IEA CC 24 YFL026W S000001868 GO:0016021 IEA CC 25 YFL026W S000001868 GO:0016021 ISM CC 26 YFL026W S000001868 GO:0019236 IEA BP 27 YFL026W S000001868 GO:0030031 IMP BP 28 YFL026W S000001868 GO:0031139 IBA BP 29 YFL026W S000001868 GO:0035624 IBA BP 30 YFL026W S000001868 GO:0038038 IBA CC 31 YFL026W S000001868 GO:0051260 IPI BP 32 YPL228W S000006149 GO:0004651 IDA MF 33 YPL228W S000006149 GO:0004651 IEA MF 34 YPL228W S000006149 GO:0005634 IEA CC 35 YPL228W S000006149 GO:0006370 IEA BP 36 YPL228W S000006149 GO:0006370 IPI BP 37 YPL228W S000006149 GO:0006397 IEA BP 38 YPL228W S000006149 GO:0016787 IEA MF 39 YPL228W S000006149 GO:0031533 IGI CC 40 YPL228W S000006149 GO:0031533 IPI CC 41 YPL228W S000006149 GO:0032968 IMP BP 42 YPL228W S000006149 GO:0098501 IDA BP 43 YPL228W S000006149 GO:0098507 IEA BP 44 YPL228W S000006149 GO:1900182 IMP BP 45 YDR110W S000002517 GO:0000183 IDA BP 46 YDR110W S000002517 GO:0000183 IMP BP 47 YDR110W S000002517 GO:0001302 IMP BP 48 YDR110W S000002517 GO:0003677 IEA MF 49 YDR110W S000002517 GO:0005634 IEA CC 50 YDR110W S000002517 GO:0005730 IDA CC 51 YDR110W S000002517 GO:0005730 IEA CC 52 YDR110W S000002517 GO:0006260 IEA BP 53 YDR110W S000002517 GO:0006310 IEA BP 54 YDR110W S000002517 GO:0006310 IMP BP 55 YDR110W S000002517 GO:0006325 IGI BP 56 YDR110W S000002517 GO:0007059 IGI BP 57 YDR110W S000002517 GO:0007580 IMP BP 58 YDR110W S000002517 GO:0008156 IDA BP 59 YDR110W S000002517 GO:0031582 IMP BP 60 YDR110W S000002517 GO:0033553 IDA CC 61 YDR110W S000002517 GO:0034503 IMP BP 62 YDR110W S000002517 GO:0043007 IGI BP 63 YDR110W S000002517 GO:0043110 IDA MF 64 YDR110W S000002517 GO:0043110 IMP MF 65 YDR110W S000002517 GO:0045911 IMP BP 66 YDR110W S000002517 GO:0046872 IEA MF 67 YDR110W S000002517 GO:0070550 IMP BP 68 YDR110W S000002517 GO:0090342 IGI BP 69 YDR110W S000002517 GO:0090342 IMP BP 70 YDR110W S000002517 GO:0090579 IMP BP 71 YPL081W S000006002 GO:0000462 IGI BP 72 YPL081W S000006002 GO:0002181 IC BP 73 YPL081W S000006002 GO:0003723 IEA MF 74 YPL081W S000006002 GO:0003735 IDA MF 75 YPL081W S000006002 GO:0003735 IEA MF 76 YPL081W S000006002 GO:0005622 IEA CC 77 YPL081W S000006002 GO:0005634 IEA CC 78 YPL081W S000006002 GO:0005730 IEA CC 79 YPL081W S000006002 GO:0005737 IDA CC 80 YPL081W S000006002 GO:0005737 IEA CC 81 YPL081W S000006002 GO:0005840 IEA CC 82 YPL081W S000006002 GO:0006364 IEA BP 83 YPL081W S000006002 GO:0006412 IEA BP 84 YPL081W S000006002 GO:0015935 IEA CC 85 YPL081W S000006002 GO:0019843 IDA MF 86 YPL081W S000006002 GO:0019843 IEA MF 87 YPL081W S000006002 GO:0019843 IMP MF 88 YPL081W S000006002 GO:0022627 IDA CC 89 YPL081W S000006002 GO:0030529 IEA CC 90 YPL081W S000006002 GO:0030686 IDA CC 91 YPL081W S000006002 GO:0032040 IDA CC 92 YPL081W S000006002 GO:0042254 IEA BP 93 YPL081W S000006002 GO:0045903 IBA BP 94 YDR204W S000002612 GO:0003674 ND MF 95 YDR204W S000002612 GO:0005739 IDA CC 96 YDR204W S000002612 GO:0005739 IEA CC 97 YDR204W S000002612 GO:0005743 IDA CC 98 YDR204W S000002612 GO:0005743 IEA CC 99 YDR204W S000002612 GO:0006744 IEA BP 100 YDR204W S000002612 GO:0006744 IMP BP 101 YDR204W S000002612 GO:0016020 IEA CC 102 YAR009C S000000067 GO:0000943 ISS CC 103 YAR009C S000000067 GO:0003676 IEA MF 104 YAR009C S000000067 GO:0003677 IEA MF 105 YAR009C S000000067 GO:0003723 IEA MF 106 YAR009C S000000067 GO:0003723 ISS MF 107 YAR009C S000000067 GO:0003824 IEA MF 108 YAR009C S000000067 GO:0003887 IEA MF 109 YAR009C S000000067 GO:0003887 ISS MF 110 YAR009C S000000067 GO:0003964 IEA MF 111 YAR009C S000000067 GO:0003964 ISS MF 112 YAR009C S000000067 GO:0004518 IEA MF 113 YAR009C S000000067 GO:0004519 IEA MF 114 YAR009C S000000067 GO:0004523 IEA MF 115 YAR009C S000000067 GO:0004540 ISS MF 116 YAR009C S000000067 GO:0005634 IDA CC 117 YAR009C S000000067 GO:0005634 IEA CC 118 YAR009C S000000067 GO:0005737 IDA CC 119 YAR009C S000000067 GO:0005737 IEA CC 120 YAR009C S000000067 GO:0006278 IEA BP 121 YAR009C S000000067 GO:0006310 IEA BP 122 YAR009C S000000067 GO:0006508 IEA BP 123 YAR009C S000000067 GO:0008152 IEA BP 124 YAR009C S000000067 GO:0008233 ISS MF 125 YAR009C S000000067 GO:0015074 IEA BP 126 YAR009C S000000067 GO:0016740 IEA MF 127 YAR009C S000000067 GO:0016779 IEA MF 128 YAR009C S000000067 GO:0016787 IEA MF 129 YAR009C S000000067 GO:0032196 IEA BP 130 YAR009C S000000067 GO:0032197 ISS BP 131 YAR009C S000000067 GO:0046872 IEA MF 132 YAR009C S000000067 GO:0071897 IEA BP 133 YAR009C S000000067 GO:0090305 IEA BP 134 YAR009C S000000067 GO:0090501 IEA BP 135 YAR009C S000000067 GO:0090502 IEA BP 136 YHR167W S000001210 GO:0000445 IMP CC 137 YHR167W S000001210 GO:0000445 IPI CC 138 YHR167W S000001210 GO:0000446 IEA CC 139 YHR167W S000001210 GO:0000446 IMP CC 140 YHR167W S000001210 GO:0000446 IPI CC 141 YHR167W S000001210 GO:0000723 IMP BP 142 YHR167W S000001210 GO:0003676 IDA MF 143 YHR167W S000001210 GO:0005634 IEA CC 144 YHR167W S000001210 GO:0006310 IMP BP 145 YHR167W S000001210 GO:0006351 IEA BP 146 YHR167W S000001210 GO:0006355 IEA BP 147 YHR167W S000001210 GO:0006368 IEA BP 148 YHR167W S000001210 GO:0006368 IMP BP 149 YHR167W S000001210 GO:0006406 IEA BP 150 YHR167W S000001210 GO:0006406 IMP BP 151 YLR390W-A S000006429 GO:0005199 IPI MF 152 YLR390W-A S000006429 GO:0005576 IEA CC 153 YLR390W-A S000006429 GO:0005618 IEA CC 154 YLR390W-A S000006429 GO:0005739 IDA CC 155 YLR390W-A S000006429 GO:0009277 IDA CC 156 YLR390W-A S000006429 GO:0016020 IEA CC 157 YLR390W-A S000006429 GO:0031225 IEA CC 158 YLR390W-A S000006429 GO:0031505 IMP BP 159 YLR390W-A S000006429 GO:0031505 ISS BP 160 YLR390W-A S000006429 GO:0071944 IDA CC 161 YLR421C S000004413 GO:0000502 IEA CC 162 YLR421C S000004413 GO:0005634 IEA CC 163 YLR421C S000004413 GO:0005737 IEA CC 164 YLR421C S000004413 GO:0006511 IMP BP 165 YLR421C S000004413 GO:0008541 IDA CC 166 YLR421C S000004413 GO:0010950 IEA BP 167 YLR421C S000004413 GO:0034515 IDA CC 168 YLR421C S000004413 GO:0043130 IDA MF 169 YLR421C S000004413 GO:0061133 IBA MF 170 YLR421C S000004413 GO:0070628 IBA MF 171 YPR089W S000006293 GO:0003674 ND MF 172 YPR089W S000006293 GO:0005575 ND CC 173 YPR089W S000006293 GO:0005794 IEA CC 174 YPR089W S000006293 GO:0008150 ND BP 175 YPL249C-A S000006438 GO:0002181 IDA BP 176 YPL249C-A S000006438 GO:0003723 IDA MF 177 YPL249C-A S000006438 GO:0003735 IDA MF 178 YPL249C-A S000006438 GO:0003735 IEA MF 179 YPL249C-A S000006438 GO:0005622 IEA CC 180 YPL249C-A S000006438 GO:0005737 IEA CC 181 YPL249C-A S000006438 GO:0005840 IEA CC 182 YPL249C-A S000006438 GO:0006412 IEA BP 183 YPL249C-A S000006438 GO:0022625 IDA CC 184 YPL249C-A S000006438 GO:0030529 IEA CC 185 YPL183W-A S000007224 GO:0003735 IEA MF 186 YPL183W-A S000007224 GO:0003735 ISA MF 187 YPL183W-A S000007224 GO:0005622 IEA CC 188 YPL183W-A S000007224 GO:0005739 IEA CC 189 YPL183W-A S000007224 GO:0005762 ISA CC 190 YPL183W-A S000007224 GO:0005840 IEA CC 191 YPL183W-A S000007224 GO:0006412 IEA BP 192 YPL183W-A S000007224 GO:0030529 IEA CC 193 YPL183W-A S000007224 GO:0032543 ISA BP 194 YPL183W-A S000007224 GO:0042254 IGI BP 195 YPL183W-A S000007224 GO:0042254 IMP BP 196 YOR298C-A S000007253 GO:0003677 IEA MF 197 YOR298C-A S000007253 GO:0003713 IDA MF 198 YOR298C-A S000007253 GO:0005634 IC CC 199 YOR298C-A S000007253 GO:0005634 IEA CC 200 YOR298C-A S000007253 GO:0005737 IEA CC [ reached getOption("max.print") -- omitted 93 rows ]
Couldn't identify where the error occurs....................
> sessionInfo() R version 3.4.4 (2018-03-15) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.1 LTS Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_IN.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_IN.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_IN.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_IN.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] rvcheck_0.1.3 org.Sc.sgd.db_3.5.0 org.Hs.eg.db_3.5.0 AnnotationDbi_1.40.0 IRanges_2.12.0 S4Vectors_0.16.0 [7] Biobase_2.38.0 BiocGenerics_0.24.0 BiocInstaller_1.28.0 GOSemSim_2.9.0 igraph_1.2.2 readr_1.3.1 [13] Matrix_1.2-15 loaded via a namespace (and not attached): [1] tidyselect_0.2.5 purrr_0.2.5 lattice_0.20-38 colorspace_1.3-2 utf8_1.1.4 blob_1.1.1 [7] rlang_0.3.0.1 pillar_1.3.1 glue_1.3.0 withr_2.1.2 DBI_1.0.0 bit64_0.9-7 [13] bindrcpp_0.2.2 bindr_0.1.1 plyr_1.8.4 MatrixModels_0.4-1 munsell_0.5.0 gtable_0.2.0 [19] devtools_2.0.1 memoise_1.1.0 knitr_1.21 curl_3.2 fansi_0.4.0 Rcpp_1.0.0 [25] scales_1.0.0 bit_1.1-14 ggplot2_3.1.0 hms_0.4.2 digest_0.6.18 dplyr_0.7.8 [31] grid_3.4.4 cli_1.0.1 tools_3.4.4 magrittr_1.5 lazyeval_0.2.1 tibble_1.4.2 [37] RSQLite_2.1.1 GO.db_3.5.0 crayon_1.3.4 pkgconfig_2.0.2 assertthat_0.2.0 httr_1.4.0 [43] rstudioapi_0.8 R6_2.3.0 compiler_3.4.4 git2r_0.23.0
pls provide `k` to make your code reproducible.