RpsiXML 2.25.0
Jitao David Zhang
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/RpsiXML |
| Branch: master |
| Last Commit: c725285 |
| Last Changed Date: 2019-02-11 08:54:05 -0400 (Mon, 11 Feb 2019) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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> library(RpsiXML)
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: XML
Loading required package: graph
Attaching package: 'graph'
The following object is masked from 'package:XML':
addNode
Loading required package: RBGL
Loading required package: hypergraph
No methods found in package 'Biobase' for request: 'listlen' when loading 'RpsiXML'
No methods found in package 'annotate' for requests: 'pubmed', 'buildPubMedAbst' when loading 'RpsiXML'
Attaching package: 'RpsiXML'
The following object is masked from 'package:IRanges':
members
> xmlDir <- system.file("/extdata/psi25files",package="RpsiXML")
>
> ## HPRD: schema check passed
> hprdxml <- file.path(xmlDir, "hprd_200709_test.xml")
> hprdSet <- parsePsimi25Interaction(hprdxml, HPRD.PSIMI25)
1 Entries found
Parsing entry 1
Parsing experiments: .........
Parsing interactors:
14% ======>
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Parsing interactions:
......
> hprdInteractors <- interactors(hprdSet)
> hprdInteractorInfo <- interactorInfo(hprdSet)
> pubmedID(hprdSet)
[1] "9443898" "7738346" "9606214" "11790773" "15140227" "12707304"
>
> ## BiOGRID: schema check failed, trivial
> gridxml <- file.path(xmlDir, "biogrid_200804_test.xml")
> gridSet <- parsePsimi25Interaction(gridxml, BIOGRID.PSIMI25)
1 Entries found
Parsing entry 1
Parsing experiments: ...
Parsing interactors:
14% ======>
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Parsing interactions:
.....
>
> ## large files
> gridLargexml <- file.path(xmlDir, "biogrid_2008_test_large.xml")
> gridHumanxml <- file.path(xmlDir, "biogrid_2008_test_human.xml")
>
> if(file.exists(gridLargexml)) {
+ Rprof("gridLarge.prof")
+ gridLargeSet <- parsePsimi25Interaction(gridLargexml, BIOGRID.PSIMI25, verbose=TRUE)
+ Rprof(NULL)
+ }
> if(file.exists(gridHumanxml)){
+ Rprof("gridHuman.prof")
+ gridHumanSet <- parsePsimi25Interaction(gridHumanxml, BIOGRID.PSIMI25)
+ Rprof(NULL)
+ }
>
> ## MINT: schema check passed
> mintxml <- file.path(xmlDir, "mint_200711_test.xml")
> mintSet <- parsePsimi25Interaction(mintxml, MINT.PSIMI25)
1 Entries found
Parsing entry 1
Parsing experiments: ..
Parsing interactors:
6% ==>
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Parsing interactions:
.................
>
> ## IntAct: schema check passed
> intactxml <- file.path(xmlDir, "intact_2008_test.xml")
> intactSet <- parsePsimi25Interaction(intactxml, INTACT.PSIMI25)
1 Entries found
Parsing entry 1
Parsing experiments: ..
Parsing interactors:
3% =>
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Parsing interactions:
.............................................................................................
> intactGraph <- psimi25XML2Graph(intactxml, INTACT.PSIMI25)
1 Entries found
Parsing entry 1
Parsing experiments: ..
Parsing interactors:
3% =>
6% ==>
10% ====>
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Parsing interactions:
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> intactGraphNew <- translateID(intactGraph,"sourceId")## translate the nodes of the graph to another identifier
> intactTestInteraction <- interactions(intactSet)[[1]]
> bait(intactTestInteraction)
[1] "A4JYL6"
> prey(intactTestInteraction)
[1] "A4JYH2"
> participant(intactTestInteraction)
A4JYH2 A4JYL6
"A4JYH2" "A4JYL6"
> inhibitor(intactTestInteraction)
[1] NA
> neutralComponent(intactTestInteraction)
[1] NA
> pubmedID(intactTestInteraction)
[1] "18296487"
> intactTestInteractor <- interactors(intactSet)[[1]]
> availableXrefs(intactTestInteractor)
[1] "sourceId" "uniprotkb" "intact"
>
> ## which cross references does the set provide?
> intactXrefs <- availableXrefs(intactSet)
> ## which references exist for every interactor?
> intactXrefIns <- availableXrefs(intactSet, intersect=TRUE)
>
> intactSetInteractors <- interactors(intactSet)
> intactXrefExample <- xref(intactSetInteractors[[1]])
> translateID(intactSetInteractors,"intact")
A4JYH2 A4JYL6 Q7ZU88 Q5J1R9 Q7SX76
"EBI-1579530" "EBI-1579616" "EBI-1579427" "EBI-1579627" "EBI-1579511"
A4JYK9 A4JYF7 A4JYL8 A4JYI5 A4JYL3
"EBI-1579400" "EBI-1579578" "EBI-1579370" "EBI-1579373" "EBI-1579353"
A4JYM3 A3KPA0 A0S0K7 A4JYP5 A4JYG4
"EBI-1579304" "EBI-1579361" "EBI-1579594" "EBI-1579664" "EBI-1579266"
A4JYF6 Q90YM1 A4JYG2 A4JYG3 P09326
"EBI-1579619" "EBI-1579680" "EBI-1579332" "EBI-1579335" "EBI-714770"
Q9BZW8 P04218 A4JYD4 Q6NW92 A4JYD8
"EBI-1580565" "EBI-915817" "EBI-1579591" "EBI-1579483" "EBI-1579656"
A4JYG1 A2CF10 A4JYF3 Q5W433 Q90413
"EBI-1579667" "EBI-1579611" "EBI-1579465" "EBI-1579381" "EBI-1579413"
A4JYS0
"EBI-1579603"
> translateID(intactSetInteractors[[1]],"intact")
[1] "EBI-1579530"
>
> intactComplexxml <- file.path(xmlDir,"intact_complexSample.xml")
> intactComplexSet <- parsePsimi25Complex(intactComplexxml, INTACT.PSIMI25)
> intactComplexGraph <- psimi25XML2Graph(intactComplexxml, INTACT.PSIMI25, type="complex")
> translateID(intactComplexGraph, "intact", "P49432")
[1] "EBI-917663"
> translateID(intactComplexGraph, "intact", NA)
<NA> <NA> <NA> <NA> <NA>
"EBI-1163494" "EBI-967760" "EBI-1225105" "EBI-1225103" "EBI-847690"
>
> complexSample <- complexes(intactComplexSet)[[2]]
> complexName(complexSample)
[1] "BAD:BCL-2 heterodimer"
> attributesList(complexSample)
[[1]]
curated-complex: BH3 domain-containing BAD interacts with and inhibits anti-apoptotic BCL-2. May act to prevent BCl-2 from sequestering BID and other pro-apoptotic molecules.
[[2]]
complex-synonym: BAD:BCL-2; BAD:BCL2; BCL-2:BAD; BCL2:BAD;
[[3]]
kd: 0.0
> members(complexSample)
sourceId uniprotId multiplicity
4 4 P10415 1
8 8 Q92934 1
>
> ## DIP: schema check failed, namespace not unique, modified
> dipxml <- file.path(xmlDir, "dip_2008_test.xml")
> dipSet <- parsePsimi25Interaction(dipxml, DIP.PSIMI25)
1 Entries found
Parsing entry 1
Parsing experiments:
Parsing interactors:
3% =>
5% ==>
8% ===>
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Parsing interactions:
............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
> dipInteractions <- interactions(dipSet)
> dipInteractionTypes <- sapply(dipInteractions, interactionType)
> stopifnot(!any(is.na(dipInteractionTypes)))
>
> ## MatrixDB
> matrixdbxml <- file.path(xmlDir, "matrixdb_20080609.xml")
> matrixdbSet <- parsePsimi25Interaction(matrixdbxml, MATRIXDB.PSIMI25)
141 Entries found
Parsing entry 1
Parsing experiments:
Parsing interactors:
50% ====================>
100% ========================================>
Parsing interactions:
.
>
> ## MIPS: schema check failed
> ##mipsxml <- file.path(xmlDir, "mips_2007_test.xml")
> ##mipsSet <- parsePsimi25Interaction(mipsxml, MIPS.PSIMI25) ## needs implementation
>
> ## CORUM:
> corumxml <- file.path(xmlDir,"corumPsimi")
> if(file.exists(corumxml)) {
+ corumSet <- parsePsimi25Interaction(corumxml,CORUM.PSIMI25, verbose=FALSE)
+ }
>
> ##############################
> ## Validating PSI-MI 2.5 Files
> ##############################
> #okFile <- system.file("extdata/psi25files/intact_2008_test.xml",
> # package="RpsiXML")
> #errorFile <- system.file("extdata/psi25files/mips_2007_test.xml",
> # package="RpsiXML")
> #mif25Schema <- system.file("extdata/schemas/MIF25.xsd",package="RpsiXML")
> #stopifnot(file.exists(okFile) &&
> # file.exists(errorFile) &&
> # file.exists(mif25Schema))
> #
> #validatePSIMI25(okFile)
> #validatePSIMI25(errorFile)
> #validatePSIMI25(errorFile, ignore.stderr=FALSE)
>
>
> proc.time()
user system elapsed
19.928 0.275 20.283