STRINGdb 1.5.5
Andrea Franceschini , Alexander Roth , Christian Von Mering , Michael Kuhn , Lars J Jensen
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/STRINGdb | | Last Changed Rev: 98967 / Revision: 102249 | | Last Changed Date: 2015-02-02 10:07:39 -0800 (Mon, 02 Feb 2015) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ ERROR ] | OK |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch STRINGdb_1.5.5.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/STRINGdb.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘STRINGdb/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘STRINGdb’ version ‘1.5.5’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘png’ ‘sqldf’ ‘plyr’ ‘igraph’ ‘RCurl’ ‘plotrix’ ‘RColorBrewer’
‘gplots’ ‘hash’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘STRINGdb’ can be installed ... [6s/6s] OK
* checking installed package size ... NOTE
installed size is 5.8Mb
sub-directories of 1Mb or more:
doc 5.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
‘RColorBrewer’ ‘RCurl’ ‘gplots’ ‘hash’ ‘igraph’ ‘methods’ ‘plotrix’
‘plyr’ ‘png’ ‘sqldf’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
get_STRING_species: no visible binding for global variable
‘official_name’
postFormSmart: no visible global function definition for ‘curlOptions’
postFormSmart: no visible global function definition for
‘getCurlHandle’
postFormSmart: no visible binding for global variable ‘curlEscape’
postFormSmart: no visible global function definition for ‘postForm’
ppi_enrichment: no visible global function definition for ‘V’
ppi_enrichment: no visible global function definition for ‘ecount’
ppi_enrichment: no visible global function definition for
‘induced.subgraph’
ppi_enrichment: no visible global function definition for ‘degree’
ppi_enrichment_full: no visible global function definition for ‘V’
ppi_enrichment_full: no visible global function definition for ‘ecount’
ppi_enrichment_full: no visible global function definition for
‘induced.subgraph’
ppi_enrichment_full: no visible global function definition for ‘degree’
ppie.getNumEdgesBetween: no visible global function definition for
‘neighborhood’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘STRINGdb-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: STRINGdb-package
> ### Title: STRINGdb (an R interface to http://string-db.org)
> ### Aliases: \S4method{STRINGdb-package}{STRINGdb}
> ### Keywords: package
>
> ### ** Examples
>
>
> library(STRINGdb)
> data(diff_exp_example1)
>
> # create a new STRING_db object
> string_db <- STRINGdb$new()
WARNING: You didn't specify a species. Hence we will set 9606 (Homo Sapiens) as your species.
WARNING: You didn't specify a version of the STRING database to use. Hence we will use STRING 9_1.
>
> # map to STRING
> example1_mapped = string_db$map( diff_exp_example1, "gene", removeUnmappedRows = TRUE )
trying URL 'http://string.uzh.ch/permanent/string/9_1/protein_aliases/9606__protein_aliases_tf.tsv.gz'
Content type 'application/x-gzip' length 12814734 bytes (12.2 MB)
opened URL
==================================================
downloaded 12.2 MB
trying URL 'http://string.uzh.ch/permanent/string/9_1/proteins/9606__proteins.tsv.gz'
Content type 'application/x-gzip' length 1826579 bytes (1.7 MB)
opened URL
==================================================
downloaded 1.7 MB
Warning: we couldn't map to STRING 17% of your identifiers>
> # get the best 200 hits
> hits = example1_mapped$STRING_id[1:200]
>
> # plot the STRING network png
> string_db$plot_network( hits )
trying URL 'http://string.uzh.ch/permanent/string/9_1/protein_links/9606__protein_links.tsv.gz'
Content type 'application/x-gzip' length 18915936 bytes (18.0 MB)
opened URL
==================================================
downloaded 18.0 MB
>
> # plot a protein-protein enrichment graph of the best 1000 hits in order to see how the ppi signal is distributed along the sorted list
> string_db$plot_ppi_enrichment( example1_mapped$STRING_id[1:1000] )
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>
>
> ######## use the "halo" mechanism in STRING to distinguish between down and up-regulated genes ########
>
> # filter by p-value and add a color column (i.e. green down-regulated gened and red for up-regulated genes)
> example1_mapped_pval05 = string_db$add_diff_exp_color( subset(example1_mapped, pvalue<0.05), logFcColStr="logFC" )
>
> # post payload information to the STRING server
> payload_id = string_db$post_payload( example1_mapped_pval05$STRING_id, colors=example1_mapped_pval05$color )
>
> # display a STRING network png with the "halo"
> string_db$plot_network( hits, payload_id=payload_id )
>
>
> ######## compute enrichment in GO annotations ########
> enrichmentGO = string_db$get_enrichment( hits, category = "Process", methodMT = "fdr", iea = TRUE )
trying URL 'http://string.uzh.ch/permanent/string/9_1/enrichment_annotations/annotations/annotations_9606.tsv.gz'
Content type 'application/x-gzip' length 21476039 bytes (20.5 MB)
opened URL
==================================================
downloaded 20.5 MB
Loading required package: tcltk
trying URL 'http://string.uzh.ch/permanent/string/9_1/enrichment_annotations/annotations_description/annotations_description.tsv.gz'
Content type 'application/x-gzip' length 24278820 bytes (23.2 MB)
opened URL
==================================================
downloaded 23.2 MB
> enrichmentKEGG = string_db$get_enrichment( hits, category = "KEGG", methodMT = "fdr", iea = TRUE )
> head(enrichmentGO, n=7)
term_id proteins hits pvalue pvalue_fdr
1 GO:0006952 1181 25 8.429187e-07 0.001672707
2 GO:0052547 301 12 1.616923e-06 0.001672707
3 GO:0043207 576 16 3.407698e-06 0.001762632
4 GO:0051707 576 16 3.407698e-06 0.001762632
5 GO:0010466 180 9 5.536201e-06 0.001977537
6 GO:0009607 605 16 6.338179e-06 0.001977537
7 GO:0052548 288 11 6.690556e-06 0.001977537
term_description
1 defense response
2 regulation of peptidase activity
3 response to external biotic stimulus
4 response to other organism
5 negative regulation of peptidase activity
6 response to biotic stimulus
7 regulation of endopeptidase activity
> head(enrichmentKEGG, n=7)
term_id proteins hits pvalue pvalue_fdr
1 hsa00512 218 10 6.603565e-10 7.792207e-08
2 hsa04115 72 7 1.519531e-09 8.965232e-08
3 hsa04512 450 12 5.404541e-09 2.125786e-07
4 hsa00500 61 5 8.987697e-07 2.651371e-05
5 hsa00140 286 8 1.652849e-06 3.280367e-05
6 hsa04610 69 5 1.667983e-06 3.280367e-05
7 hsa04145 227 7 4.080518e-06 6.878588e-05
term_description
1 Mucin type O-Glycan biosynthesis
2 p53 signaling pathway
3 ECM-receptor interaction
4 Starch and sucrose metabolism
5 Steroid hormone biosynthesis
6 Complement and coagulation cascades
7 Phagosome
>
>
>
> ######## Use STRING in order to get homologous proteins in other species ########
>
> # get the reciprocal best hits of the following protein in all the STRING species
> string_db$get_homologs_besthits(c("9606.ENSP00000365757"), symbets = TRUE)
STRING_id species_id best_hit_STRING_id best_hit_bitscore
1 9606.ENSP00000365757 6085 6085.XP_002161268 480.5
2 9606.ENSP00000365757 6238 6238.CBG15109 455.7
3 9606.ENSP00000365757 6239 6239.Y48G9A.8 476.6
4 9606.ENSP00000365757 6945 6945.ISCW009432-PA 467.2
5 9606.ENSP00000365757 7070 7070.XP_971403 572.6
6 9606.ENSP00000365757 7719 7719.ENSCINP00000013390 546.4
7 9606.ENSP00000365757 7955 7955.ENSDARP00000003352 816.7
8 9606.ENSP00000365757 8090 8090.ENSORLP00000009006 808.3
9 9606.ENSP00000365757 9031 9031.ENSGALP00000012779 791.9
10 9606.ENSP00000365757 9258 9258.ENSOANP00000009063 835.9
11 9606.ENSP00000365757 9361 9361.ENSDNOP00000012412 716.1
12 9606.ENSP00000365757 9544 9544.ENSMMUP00000019705 836.9
13 9606.ENSP00000365757 9598 9598.ENSPTRP00000003988 836.9
14 9606.ENSP00000365757 9600 9600.ENSPPYP00000002495 849.1
15 9606.ENSP00000365757 9606 9606.ENSP00000365757 944.1
16 9606.ENSP00000365757 9615 9615.ENSCAFP00000006237 836.9
17 9606.ENSP00000365757 9685 9685.ENSFCAP00000005093 750.0
18 9606.ENSP00000365757 9796 9796.ENSECAP00000006272 830.6
19 9606.ENSP00000365757 9823 9823.ENSSSCP00000011817 940.6
20 9606.ENSP00000365757 9913 9913.ENSBTAP00000024007 828.5
21 9606.ENSP00000365757 9986 9986.ENSOCUP00000014710 943.8
22 9606.ENSP00000365757 10090 10090.ENSMUSP00000006912 934.0
23 9606.ENSP00000365757 10141 10141.ENSCPOP00000006815 925.6
24 9606.ENSP00000365757 10228 10228.JGI22804 468.9
25 9606.ENSP00000365757 13616 13616.ENSMODP00000011260 931.2
26 9606.ENSP00000365757 28377 28377.ENSACAP00000008733 780.0
27 9606.ENSP00000365757 31033 31033.ENSTRUP00000005623 811.8
28 9606.ENSP00000365757 31234 31234.CRE02385 477.3
29 9606.ENSP00000365757 35128 35128.JGI264335 189.3
30 9606.ENSP00000365757 59729 59729.ENSTGUP00000001234 795.4
31 9606.ENSP00000365757 67593 67593.JGI138693 190.7
32 9606.ENSP00000365757 69293 69293.ENSGACP00000003246 794.3
33 9606.ENSP00000365757 135651 135651.CBN14981 476.3
34 9606.ENSP00000365757 281687 281687.CJA09616 425.6
35 9606.ENSP00000365757 317025 317025.Tcr_0057 53.8
best_hit_normscore best_hit_alignment_length nr_high_scoring_hits
1 0.5089500 396 2
2 0.4826820 391 3
3 0.5048190 392 3
4 0.4948630 359 4
5 0.6065040 409 3
6 0.5787520 391 4
7 0.8650570 403 11
8 0.8561590 404 10
9 0.8387880 357 6
10 0.8853940 382 6
11 0.7585000 357 5
12 0.8864530 357 6
13 0.8864530 357 8
14 0.8993750 362 9
15 1.0000000 405 9
16 0.8864530 357 9
17 0.7944070 404 6
18 0.8797800 357 7
19 0.9962930 405 5
20 0.8775550 356 8
21 0.9996820 405 7
22 0.9893020 404 8
23 0.9804050 402 8
24 0.4966630 386 2
25 0.9863360 405 7
26 0.8261840 356 7
27 0.8598670 404 13
28 0.5055610 385 4
29 0.2005080 323 4
30 0.8424960 357 6
31 0.2019910 294 15
32 0.8413300 403 13
33 0.5045020 392 5
34 0.4508000 406 3
35 0.0569855 205 0
>
> # get the homologs of the following two proteins in the mouse (i.e. species_id=10090)
> string_db$get_homologs(c("9606.ENSP00000365757", "9606.ENSP00000352336"), target_species_id=10090, bitscore_threshold=60)
STRING_id_a STRING_id_b bitscore start_a end_a start_b
1 9606.ENSP00000352336 10090.ENSMUSP00000003370 73.0 530 695 140
2 9606.ENSP00000352336 10090.ENSMUSP00000004377 76.2 531 722 4
3 9606.ENSP00000352336 10090.ENSMUSP00000004959 85.6 640 827 57
4 9606.ENSP00000352336 10090.ENSMUSP00000005889 85.9 646 826 671
5 9606.ENSP00000352336 10090.ENSMUSP00000006293 61.2 532 825 14
6 9606.ENSP00000352336 10090.ENSMUSP00000010804 303.8 30 478 28
7 9606.ENSP00000352336 10090.ENSMUSP00000014597 75.5 514 680 99
8 9606.ENSP00000352336 10090.ENSMUSP00000016498 66.7 638 739 127
9 9606.ENSP00000352336 10090.ENSMUSP00000016511 65.3 642 734 74
10 9606.ENSP00000352336 10090.ENSMUSP00000017920 66.4 637 830 4
11 9606.ENSP00000352336 10090.ENSMUSP00000019913 70.6 511 649 101
12 9606.ENSP00000352336 10090.ENSMUSP00000020564 61.2 454 631 367
13 9606.ENSP00000352336 10090.ENSMUSP00000021090 96.8 640 828 57
14 9606.ENSP00000352336 10090.ENSMUSP00000025912 192.1 810 1198 479
15 9606.ENSP00000352336 10090.ENSMUSP00000025962 223.8 207 1182 1269
16 9606.ENSP00000352336 10090.ENSMUSP00000027888 67.8 517 648 157
17 9606.ENSP00000352336 10090.ENSMUSP00000028252 61.9 526 618 431
18 9606.ENSP00000352336 10090.ENSMUSP00000029806 64.6 646 769 35
19 9606.ENSP00000352336 10090.ENSMUSP00000030464 75.5 370 640 198
20 9606.ENSP00000352336 10090.ENSMUSP00000030693 71.3 517 621 116
21 9606.ENSP00000352336 10090.ENSMUSP00000032356 219.0 145 487 13
22 9606.ENSP00000352336 10090.ENSMUSP00000032931 61.5 731 831 549
23 9606.ENSP00000352336 10090.ENSMUSP00000033468 71.3 771 888 185
24 9606.ENSP00000352336 10090.ENSMUSP00000034296 67.8 637 795 315
25 9606.ENSP00000352336 10090.ENSMUSP00000034745 62.2 767 827 1050
26 9606.ENSP00000352336 10090.ENSMUSP00000034863 65.3 532 806 82
27 9606.ENSP00000352336 10090.ENSMUSP00000036270 107.6 635 826 661
28 9606.ENSP00000352336 10090.ENSMUSP00000037854 245.8 4 478 13
29 9606.ENSP00000352336 10090.ENSMUSP00000038838 74.4 530 673 127
30 9606.ENSP00000352336 10090.ENSMUSP00000046532 80.7 512 824 41
31 9606.ENSP00000352336 10090.ENSMUSP00000046584 262.3 48 478 169
32 9606.ENSP00000352336 10090.ENSMUSP00000048057 60.5 636 754 8
33 9606.ENSP00000352336 10090.ENSMUSP00000056774 67.4 641 735 619
34 9606.ENSP00000352336 10090.ENSMUSP00000058757 107.9 531 787 5
35 9606.ENSP00000352336 10090.ENSMUSP00000059658 63.6 642 735 389
36 9606.ENSP00000352336 10090.ENSMUSP00000060433 61.9 626 740 384
37 9606.ENSP00000352336 10090.ENSMUSP00000060828 74.4 641 862 162
38 9606.ENSP00000352336 10090.ENSMUSP00000062782 94.0 634 826 647
39 9606.ENSP00000352336 10090.ENSMUSP00000066209 69.5 433 790 47
40 9606.ENSP00000352336 10090.ENSMUSP00000066361 63.2 763 831 1149
41 9606.ENSP00000352336 10090.ENSMUSP00000072154 69.9 517 638 140
42 9606.ENSP00000352336 10090.ENSMUSP00000072840 69.5 778 909 8
43 9606.ENSP00000352336 10090.ENSMUSP00000075167 70.6 517 648 130
44 9606.ENSP00000352336 10090.ENSMUSP00000079991 2832.2 1 1265 1
45 9606.ENSP00000352336 10090.ENSMUSP00000081122 313.9 54 1243 53
46 9606.ENSP00000352336 10090.ENSMUSP00000084679 60.8 759 827 436
47 9606.ENSP00000352336 10090.ENSMUSP00000091940 62.6 518 635 470
48 9606.ENSP00000352336 10090.ENSMUSP00000092252 62.6 1027 1161 1
49 9606.ENSP00000352336 10090.ENSMUSP00000097547 76.9 517 680 133
50 9606.ENSP00000352336 10090.ENSMUSP00000099366 280.8 67 480 107
51 9606.ENSP00000352336 10090.ENSMUSP00000099404 1468.2 11 1242 18
52 9606.ENSP00000352336 10090.ENSMUSP00000099583 185.8 54 457 49
53 9606.ENSP00000352336 10090.ENSMUSP00000101256 329.6 21 1182 122
54 9606.ENSP00000352336 10090.ENSMUSP00000104860 62.6 637 765 236
55 9606.ENSP00000352336 10090.ENSMUSP00000105155 62.2 517 666 140
56 9606.ENSP00000352336 10090.ENSMUSP00000105179 85.6 506 883 149
57 9606.ENSP00000352336 10090.ENSMUSP00000105189 60.1 532 680 93
58 9606.ENSP00000352336 10090.ENSMUSP00000105736 216.2 52 460 48
59 9606.ENSP00000352336 10090.ENSMUSP00000105743 193.8 54 457 54
60 9606.ENSP00000352336 10090.ENSMUSP00000106539 70.2 771 965 165
61 9606.ENSP00000352336 10090.ENSMUSP00000109234 65.3 646 858 150
62 9606.ENSP00000352336 10090.ENSMUSP00000109377 272.0 65 480 61
63 9606.ENSP00000352336 10090.ENSMUSP00000112221 61.9 645 726 281
64 9606.ENSP00000352336 10090.ENSMUSP00000117099 64.3 632 740 335
65 9606.ENSP00000352336 10090.ENSMUSP00000118491 62.2 759 827 404
66 9606.ENSP00000365757 10090.ENSMUSP00000006912 934.0 1 405 1
67 9606.ENSP00000365757 10090.ENSMUSP00000013970 600.2 16 405 26
68 9606.ENSP00000365757 10090.ENSMUSP00000018691 743.4 13 406 18
69 9606.ENSP00000365757 10090.ENSMUSP00000025800 199.4 33 401 25
70 9606.ENSP00000365757 10090.ENSMUSP00000038225 195.2 34 401 76
71 9606.ENSP00000365757 10090.ENSMUSP00000051282 119.8 98 397 107
72 9606.ENSP00000365757 10090.ENSMUSP00000102852 199.4 34 401 68
73 9606.ENSP00000365757 10090.ENSMUSP00000109676 88.0 91 282 1773
end_b size_b
1 285 524
2 197 596
3 215 217
4 839 845
5 292 303
6 471 756
7 246 499
8 231 507
9 169 451
10 193 304
11 237 512
12 540 548
13 214 217
14 857 1234
15 1963 2282
16 272 1182
17 519 538
18 164 280
19 457 461
20 218 517
21 333 647
22 655 764
23 305 788
24 475 722
25 1107 1107
26 352 450
27 845 847
28 487 1015
29 252 512
30 317 322
31 596 1128
32 136 1257
33 718 724
34 272 597
35 488 492
36 503 503
37 388 629
38 864 868
39 354 509
40 1214 1719
41 258 541
42 137 709
43 245 1142
44 1265 1265
45 920 1682
46 508 513
47 575 579
48 126 825
49 282 537
50 503 785
51 1267 1302
52 464 1181
53 958 1501
54 368 625
55 273 541
56 558 1038
57 248 259
58 467 1175
59 468 1216
60 371 862
61 380 527
62 456 807
63 362 377
64 446 446
65 476 481
66 405 405
67 420 421
68 416 416
69 391 539
70 439 661
71 386 395
72 431 547
73 1979 2052
>
>
>
> ######## Retrieve protein-protein interactions ########
>
> # get the neighbors (in the ppi graph) of a given protein(s)
> string_db$get_neighbors(c("9606.ENSP00000365757", "9606.ENSP00000352336"))
[1] "9606.ENSP00000007390" "9606.ENSP00000162749" "9606.ENSP00000171887"
[4] "9606.ENSP00000195649" "9606.ENSP00000201586" "9606.ENSP00000211998"
[7] "9606.ENSP00000216117" "9606.ENSP00000216277" "9606.ENSP00000219789"
[10] "9606.ENSP00000221283" "9606.ENSP00000222124" "9606.ENSP00000222254"
[13] "9606.ENSP00000223023" "9606.ENSP00000225504" "9606.ENSP00000225655"
[16] "9606.ENSP00000230124" "9606.ENSP00000230449" "9606.ENSP00000230859"
[19] "9606.ENSP00000234313" "9606.ENSP00000239940" "9606.ENSP00000240132"
[22] "9606.ENSP00000240139" "9606.ENSP00000240327" "9606.ENSP00000243924"
[25] "9606.ENSP00000244007" "9606.ENSP00000246062" "9606.ENSP00000249071"
[28] "9606.ENSP00000249647" "9606.ENSP00000249700" "9606.ENSP00000249861"
[31] "9606.ENSP00000250699" "9606.ENSP00000252699" "9606.ENSP00000253083"
[34] "9606.ENSP00000253861" "9606.ENSP00000254806" "9606.ENSP00000255039"
[37] "9606.ENSP00000255882" "9606.ENSP00000256190" "9606.ENSP00000259271"
[40] "9606.ENSP00000260257" "9606.ENSP00000260386" "9606.ENSP00000260402"
[43] "9606.ENSP00000260762" "9606.ENSP00000260766" "9606.ENSP00000261349"
[46] "9606.ENSP00000261776" "9606.ENSP00000262033" "9606.ENSP00000262039"
[49] "9606.ENSP00000262139" "9606.ENSP00000262445" "9606.ENSP00000262713"
[52] "9606.ENSP00000262717" "9606.ENSP00000262741" "9606.ENSP00000263125"
[55] "9606.ENSP00000263168" "9606.ENSP00000263967" "9606.ENSP00000264380"
[58] "9606.ENSP00000264414" "9606.ENSP00000264710" "9606.ENSP00000265382"
[61] "9606.ENSP00000265741" "9606.ENSP00000265960" "9606.ENSP00000266087"
[64] "9606.ENSP00000266505" "9606.ENSP00000267101" "9606.ENSP00000267615"
[67] "9606.ENSP00000269025" "9606.ENSP00000269159" "9606.ENSP00000269300"
[70] "9606.ENSP00000269321" "9606.ENSP00000270202" "9606.ENSP00000271657"
[73] "9606.ENSP00000272102" "9606.ENSP00000272298" "9606.ENSP00000272427"
[76] "9606.ENSP00000274335" "9606.ENSP00000275198" "9606.ENSP00000276410"
[79] "9606.ENSP00000278279" "9606.ENSP00000279230" "9606.ENSP00000281038"
[82] "9606.ENSP00000282074" "9606.ENSP00000284384" "9606.ENSP00000284523"
[85] "9606.ENSP00000285419" "9606.ENSP00000285600" "9606.ENSP00000286317"
[88] "9606.ENSP00000286428" "9606.ENSP00000289153" "9606.ENSP00000290846"
[91] "9606.ENSP00000291295" "9606.ENSP00000292807" "9606.ENSP00000295024"
[94] "9606.ENSP00000295057" "9606.ENSP00000296003" "9606.ENSP00000296794"
[97] "9606.ENSP00000297029" "9606.ENSP00000298229" "9606.ENSP00000298316"
[100] "9606.ENSP00000298642" "9606.ENSP00000298841" "9606.ENSP00000300935"
[103] "9606.ENSP00000302005" "9606.ENSP00000302276" "9606.ENSP00000303476"
[106] "9606.ENSP00000304283" "9606.ENSP00000305011" "9606.ENSP00000305958"
[109] "9606.ENSP00000306124" "9606.ENSP00000306382" "9606.ENSP00000307183"
[112] "9606.ENSP00000307356" "9606.ENSP00000307684" "9606.ENSP00000308176"
[115] "9606.ENSP00000308622" "9606.ENSP00000310969" "9606.ENSP00000312734"
[118] "9606.ENSP00000313121" "9606.ENSP00000313731" "9606.ENSP00000314311"
[121] "9606.ENSP00000314458" "9606.ENSP00000316029" "9606.ENSP00000317334"
[124] "9606.ENSP00000317985" "9606.ENSP00000319322" "9606.ENSP00000319511"
[127] "9606.ENSP00000319601" "9606.ENSP00000319654" "9606.ENSP00000320025"
[130] "9606.ENSP00000322170" "9606.ENSP00000322234" "9606.ENSP00000323377"
[133] "9606.ENSP00000323927" "9606.ENSP00000324806" "9606.ENSP00000325423"
[136] "9606.ENSP00000326514" "9606.ENSP00000328773" "9606.ENSP00000329127"
[139] "9606.ENSP00000331313" "9606.ENSP00000331602" "9606.ENSP00000334105"
[142] "9606.ENSP00000334416" "9606.ENSP00000334490" "9606.ENSP00000335333"
[145] "9606.ENSP00000338185" "9606.ENSP00000339826" "9606.ENSP00000340017"
[148] "9606.ENSP00000340093" "9606.ENSP00000340896" "9606.ENSP00000341243"
[151] "9606.ENSP00000341680" "9606.ENSP00000342510" "9606.ENSP00000342935"
[154] "9606.ENSP00000344488" "9606.ENSP00000344818" "9606.ENSP00000345083"
[157] "9606.ENSP00000345206" "9606.ENSP00000345988" "9606.ENSP00000346453"
[160] "9606.ENSP00000347198" "9606.ENSP00000347244" "9606.ENSP00000347792"
[163] "9606.ENSP00000347931" "9606.ENSP00000348010" "9606.ENSP00000348461"
[166] "9606.ENSP00000348602" "9606.ENSP00000348984" "9606.ENSP00000348986"
[169] "9606.ENSP00000349205" "9606.ENSP00000349275" "9606.ENSP00000349467"
[172] "9606.ENSP00000350649" "9606.ENSP00000350698" "9606.ENSP00000350928"
[175] "9606.ENSP00000350941" "9606.ENSP00000351190" "9606.ENSP00000351997"
[178] "9606.ENSP00000352035" "9606.ENSP00000352121" "9606.ENSP00000352312"
[181] "9606.ENSP00000352336" "9606.ENSP00000352834" "9606.ENSP00000353154"
[184] "9606.ENSP00000353275" "9606.ENSP00000353422" "9606.ENSP00000354519"
[187] "9606.ENSP00000354558" "9606.ENSP00000354947" "9606.ENSP00000354977"
[190] "9606.ENSP00000355537" "9606.ENSP00000355596" "9606.ENSP00000356989"
[193] "9606.ENSP00000357583" "9606.ENSP00000357674" "9606.ENSP00000357748"
[196] "9606.ENSP00000357883" "9606.ENSP00000359025" "9606.ENSP00000359417"
[199] "9606.ENSP00000359423" "9606.ENSP00000359425" "9606.ENSP00000359665"
[202] "9606.ENSP00000360076" "9606.ENSP00000360154" "9606.ENSP00000360473"
[205] "9606.ENSP00000360777" "9606.ENSP00000361021" "9606.ENSP00000362115"
[208] "9606.ENSP00000362399" "9606.ENSP00000362924" "9606.ENSP00000364287"
[211] "9606.ENSP00000365103" "9606.ENSP00000365637" "9606.ENSP00000365687"
[214] "9606.ENSP00000366272" "9606.ENSP00000366460" "9606.ENSP00000366563"
[217] "9606.ENSP00000367075" "9606.ENSP00000367276" "9606.ENSP00000367415"
[220] "9606.ENSP00000367747" "9606.ENSP00000367792" "9606.ENSP00000368086"
[223] "9606.ENSP00000370912" "9606.ENSP00000371221" "9606.ENSP00000371577"
[226] "9606.ENSP00000373347" "9606.ENSP00000373399" "9606.ENSP00000373648"
[229] "9606.ENSP00000373713" "9606.ENSP00000375928" "9606.ENSP00000376440"
[232] "9606.ENSP00000376946" "9606.ENSP00000376966" "9606.ENSP00000377148"
[235] "9606.ENSP00000377941" "9606.ENSP00000378306" "9606.ENSP00000378323"
[238] "9606.ENSP00000379372" "9606.ENSP00000379709" "9606.ENSP00000381102"
[241] "9606.ENSP00000381293" "9606.ENSP00000383457" "9606.ENSP00000384651"
[244] "9606.ENSP00000388631" "9606.ENSP00000389934" "9606.ENSP00000392147"
[247] "9606.ENSP00000393835" "9606.ENSP00000397181" "9606.ENSP00000398036"
[250] "9606.ENSP00000407333" "9606.ENSP00000408089" "9606.ENSP00000409572"
[253] "9606.ENSP00000409637" "9606.ENSP00000413780" "9606.ENSP00000414138"
[256] "9606.ENSP00000416320" "9606.ENSP00000418111"
>
> # get the interactions in between the input proteins
> string_db$get_interactions(c("9606.ENSP00000365757", "9606.ENSP00000352336"))
from to neighborhood fusion cooccurence
1 9606.ENSP00000352336 9606.ENSP00000365757 0 0 0
coexpression experimental database textmining combined_score
1 0 0 900 76 901
>
>
>
> ######## Find clusters of interactions ########
>
> # get clusters
> clustersList = string_db$get_clusters(example1_mapped$STRING_id[1:600])
>
> # plot first 4 clusters
> par(mfrow=c(2,2))
> for(i in seq(1:4)){
+ string_db$plot_network(clustersList[[i]])
+ }
Error: Proxy Error
Execution halted