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athirak1986
•
0
@athirak1986-19127
Last seen 5.4 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.