Gene similarity by GOSemSim
0
0
Entering edit mode
@athirak1986-19127
Last seen 2.5 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    
gosemsim mgenesim • 335 views
ADD COMMENT
0
Entering edit mode

pls provide `k` to make your code reproducible.

ADD REPLY

Login before adding your answer.

Traffic: 373 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6