version 0.97

torgeiou · Aug 8, 2012 · 7088e08 · 7088e08
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,14 +1,22 @@
 Package: iRefR
-Version: 0.94
-Date: 2011-11-24
+Version: 0.97
+Date: 2012-08-08
 Title: iRefIndex Manager
-Description: "iRefR" allows the user to load any version of the consolidated protein interaction database "iRefIndex" and perform tasks such as: selecting databases, pmids, experimental methods, searching for specific proteins, separate binary interactions from complexes and polymers, generate complexes according to an algorithm that looks after possible binary-represented complexes, make general database statistics and create network graphs, among others.
-Author: Antonio Mora <[email protected]>, Ian Donaldson <[email protected]>
-Maintainer: Antonio Mora <[email protected]>
-Depends: R (>= 2.12.1), graph, RBGL, igraph
+Description: "iRefR" allows the user to load any version of the
+        consolidated protein interaction database "iRefIndex" and
+        perform tasks such as: selecting databases, pmids, experimental
+        methods, searching for specific proteins, separate binary
+        interactions from complexes and polymers, generate complexes
+        according to an algorithm that looks after possible
+        binary-represented complexes, make general database statistics
+        and create network graphs, among others.
+Author: Antonio Mora <[email protected]>, Ian Donaldson
+        <[email protected]>
+Maintainer: Antonio Mora <[email protected]>
+Depends: R (>= 2.12.1), igraph (>= 0.6), graph, RBGL
 License: GPL (>= 2)
-URL: http://donaldson.uio.no/
+URL: http://donaldson.uio.no/wiki/iRefR
 BuildVignettes: FALSE
-Packaged: 2011-11-24 13:33:20 UTC; antonimo
+Packaged: 2012-08-10 11:32:16 UTC; antonimo
 Repository: CRAN
-Date/Publication: 2011-11-24 15:01:23
+Date/Publication: 2012-08-10 12:38:08
diff --git a/MD5 b/MD5
@@ -1,4 +1,4 @@
-89e194f0a71e6be1eefae032d72f9435 *DESCRIPTION
+c28c2adeaf60485ae664383cbba1de9a *DESCRIPTION
 7bb7de2a8dbc0444ba46e389bb40a2e5 *NAMESPACE
 2b460524de8f664d1b8718e3c8965803 *R/convert_MITAB_to_complexList.R
 f331958d521298155d4eb60f9ee79969 *R/convert_MITAB_to_edgeList.R
@@ -7,7 +7,7 @@ db7c7dc39451b2ffabd934a8fca0c034 *R/convert_complexList_to_MITAB.R
 e9b6720ce0e52ea7a596c4ad3c9c4834 *R/convert_edgeList_to_graph.R
 5e316910a9ef70355a096a8140220588 *R/convert_graph_to_edgeList.R
 f9a108c26d98e92050de943fe2a6a489 *R/convert_protein_ID.R
-c3bbd3c85b9e0628dd1201ae798b1404 *R/create_id_conversion_table.R
+432ce4c532b83b08213c9065a307b216 *R/create_id_conversion_table.R
 2d7e466fa43f4a63b0d61ef895b127f9 *R/get_irefindex.R
 a82e83f2525e8fe531de42a90bacc276 *R/merge_complexes_lists.R
 b2739230c622110f897247c70bba7ff3 *R/select_confidence.R
@@ -17,22 +17,22 @@ a27d7d07925296a503cdd9e347595207 *R/select_protein.R
 6f2952abe8fe62faa150e50bb238bb49 *R/summary_graph.R
 4d96d51a071f26a3079d1e0acbdeb1c9 *R/summary_protein.R
 be318d2b797b2db78035e55e6a65dff6 *R/summary_table.R
-f2c680e362ef8c8d4d2a7d0e3a5094f1 *inst/NEWS
-541ded6f062086e5af842fc6b0c9b8e6 *inst/doc/iRefR_tutorial.pdf
-53b339610669b378ac4608c62194cc10 *man/convert_MITAB_to_complexList.Rd
+40c5b3ec99a35ebf12754448e1dafd7a *inst/NEWS
+383ef36e7860e364147b440f54afe9dd *inst/doc/iRefR_tutorial.pdf
+559b72d4b564bdf9a00697334b4d4509 *man/convert_MITAB_to_complexList.Rd
 cba5669023733267af8c259df510ac35 *man/convert_MITAB_to_edgeList.Rd
-027f4845d86d4b57aecd42d9de6536c5 *man/convert_complexList_to_MITAB.Rd
+3474d71717504bbda475651bb293d029 *man/convert_complexList_to_MITAB.Rd
 89a6f9f6342d68501e238911b011693e *man/convert_edgeList_to_MITAB.Rd
-eadc69260ac36221731f38376c80278a *man/convert_edgeList_to_graph.Rd
+09077fdffdde1a75bd1f4f493a712ac3 *man/convert_edgeList_to_graph.Rd
 e27f3d901144ffe5eccfcc4724f7ccf3 *man/convert_graph_to_edgeList.Rd
 f5d862e723919b3e3f5685bd0843c441 *man/convert_protein_ID.Rd
-86c92ef49992cab4805302a3159a5b1c *man/create_id_conversion_table.Rd
+129578aee1c5e0454bee4e09334ffc2a *man/create_id_conversion_table.Rd
 cf7c693721da4f46a0dd9a8d7046becc *man/get_irefindex.Rd
-172060be03a740cc981973151418ac36 *man/merge_complexes_lists.Rd
+eb6c4e516aef88e0fbd44e7fc52f1757 *man/merge_complexes_lists.Rd
 c6973e5c7393777933839e7470b8356f *man/select_confidence.Rd
 5cd9cbfec22f4b1ec61b32e3de301a75 *man/select_database.Rd
 565c320d27d5da30f3bee6dca410728d *man/select_interaction_type.Rd
-a2db46d63943e1ccbec6609e931b5e3f *man/select_protein.Rd
+6ea12aa6b31d75b33dc2d616cea91ffe *man/select_protein.Rd
 a7d6c97fd9256f0cdc0e532baa72ccb6 *man/summary_graph.Rd
-e83453e897147bf990b14b2f2880e599 *man/summary_protein.Rd
+8d70a1b7900e7aadec6a836735a874d3 *man/summary_protein.Rd
 bdba97f5f54e8d8611a2266771a29262 *man/summary_table.Rd
diff --git a/R/create_id_conversion_table.R b/R/create_id_conversion_table.R
@@ -1,7 +1,7 @@
 ####
 # Generate a lookup table to convert any major protein ID to another protein ID:
 ####
-create_id_conversion_table = function(MITAB_table, data_folder="data", output_filename="id_conversion_table", IDs_to_include=c("uniprotkb", "refseq", "entrezgene/locuslink")) {
+create_id_conversion_table = function(MITAB_table, data_folder=getwd(), output_filename="id_conversion_table", IDs_to_include=c("uniprotkb", "refseq", "entrezgene/locuslink")) {
 
 	# 1. Constructing output file names:
 	if (data_folder == "data") {

diff --git a/inst/NEWS b/inst/NEWS
@@ -1,3 +1,69 @@
+CHANGES IN iRefR VERSION 0.97:
+
+  SIGNIFICANT USER-VISIBLE CHANGES:
+
+    • None.
+
+  NEW FEATURES:
+
+    • None.
+
+  DEPRECATED & DEFUNCT:
+
+    • None.
+
+  INSTALLATION:
+
+    • None.
+
+  BUG FIXES:
+
+    • Minor changes to follow the size and execution time policies of CRAN.
+
+CHANGES IN iRefR VERSION 0.96:
+
+  SIGNIFICANT USER-VISIBLE CHANGES:
+
+    • iRefR depends again from "igraph", which has changed and now considers all vectors starting from position one and not from position zero. From now on, "iRefR" will depend on "igraph" 0.6 or higher. The "iRefR and igraph" tutorial was also changed accordingly (see: ftp://ftp.no.embnet.org/irefindex/iRefR/current/).
+
+  NEW FEATURES:
+
+    • None.
+
+  DEPRECATED & DEFUNCT:
+
+    • None.
+
+  INSTALLATION:
+
+    • None.
+
+  BUG FIXES:
+
+    • Minor change to create_id_conversion_table: Now the default option is getwd().
+
+CHANGES IN iRefR VERSION 0.95:
+
+  SIGNIFICANT USER-VISIBLE CHANGES:
+
+    • Temporarily, iRefR will not depend on "igraph" but on "igraph0" instead. This is due to the fact that the announced next version of "igraph" will be incompatible with the previous one, and the igraph maintainers have kept the old version as a package called "igraph0", i.e., "igraph0" is identical to "igraph" v.0.5.5. When the new igraph is released and tested, we may use "igraph" again.
+
+  NEW FEATURES:
+
+    • None.
+
+  DEPRECATED & DEFUNCT:
+
+    • None.
+
+  INSTALLATION:
+
+    • None.
+
+  BUG FIXES:
+
+    • None.
+
 CHANGES IN iRefR VERSION 0.94:
 
   SIGNIFICANT USER-VISIBLE CHANGES:

diff --git a/inst/doc/iRefR_tutorial.pdf b/inst/doc/iRefR_tutorial.pdf
diff --git a/man/convert_MITAB_to_complexList.Rd b/man/convert_MITAB_to_complexList.Rd
@@ -26,7 +26,8 @@ On iROGs and icROGs:
      \item{complexList}{iRefIndex/complexList R table corresponding to the original MITAB table.}
      }
      \author{Antonio Mora <a.m.ortiz@biotek.uio.no>}
-     \examples{
+     \examples{
+     \dontrun{
      ## get tables
      irefindex_curr_ecoli = get_irefindex("562", "current", tempdir())
      iRef_binary = select_interaction_type("binary", irefindex_curr_ecoli)
@@ -35,12 +36,13 @@ On iROGs and icROGs:
      known_complexes_ecoli_complexList = convert_MITAB_to_complexList(irefindex_curr_ecoli, canonical_rep="yes", include_generated_complexes="no")
 
      ## more examples
-     #generated_complexes_ecoli_complexList = convert_MITAB_to_complexList(iRef_binary, canonical_rep="yes", include_generated_complexes="yes", list_methods="default")
-     #all_complexes_ecoli_complexList = convert_MITAB_to_complexList(irefindex_curr_ecoli, canonical_rep="yes", include_generated_complexes="yes", list_methods="default")
-     #number_unique_complexes_all = length(unique(all_complexes_ecoli_complexList[,2]))
+     generated_complexes_ecoli_complexList = convert_MITAB_to_complexList(iRef_binary, canonical_rep="yes", include_generated_complexes="yes", list_methods="default")
+     all_complexes_ecoli_complexList = convert_MITAB_to_complexList(irefindex_curr_ecoli, canonical_rep="yes", include_generated_complexes="yes", list_methods="default")
+     number_unique_complexes_all = length(unique(all_complexes_ecoli_complexList[,2]))
 
-     #known_complexes_ecoli_complexList_extended = convert_MITAB_to_complexList(irefindex_curr_ecoli, canonical_rep="yes", include_generated_complexes="no", list_methods="default", bait_use="include_non_baits")
-     #generated_complexes_ecoli_complexList_extended = convert_MITAB_to_complexList(iRef_binary, canonical_rep="yes", include_generated_complexes="yes", list_methods="default", bait_use="include_non_baits")
-     #all_complexes_ecoli_complexList_extended = convert_MITAB_to_complexList(irefindex_curr_ecoli, canonical_rep="yes", include_generated_complexes="yes", list_methods="default", bait_use="include_non_baits")
-     #number_unique_complexes_all_extended = length(unique(all_complexes_ecoli_complexList_extended[,2]))
+     known_complexes_ecoli_complexList_extended = convert_MITAB_to_complexList(irefindex_curr_ecoli, canonical_rep="yes", include_generated_complexes="no", list_methods="default", bait_use="include_non_baits")
+     generated_complexes_ecoli_complexList_extended = convert_MITAB_to_complexList(iRef_binary, canonical_rep="yes", include_generated_complexes="yes", list_methods="default", bait_use="include_non_baits")
+     all_complexes_ecoli_complexList_extended = convert_MITAB_to_complexList(irefindex_curr_ecoli, canonical_rep="yes", include_generated_complexes="yes", list_methods="default", bait_use="include_non_baits")
+     number_unique_complexes_all_extended = length(unique(all_complexes_ecoli_complexList_extended[,2]))
+     }
      }
diff --git a/man/convert_complexList_to_MITAB.Rd b/man/convert_complexList_to_MITAB.Rd
@@ -24,6 +24,7 @@ On iROGs and icROGs:
      }
      \author{Antonio Mora <a.m.ortiz@biotek.uio.no>}
      \examples{
+     \dontrun{
      ## get tables
      irefindex_curr_ecoli = get_irefindex("562", "current", tempdir())
      iRef_binary = select_interaction_type("binary", irefindex_curr_ecoli)
@@ -35,13 +36,14 @@ On iROGs and icROGs:
      setequal(dim(iRef_complex), dim(reconstructed_known_ecoli_MITAB))
 
      ## more examples
-     #generated_complexes_ecoli_complexList = convert_MITAB_to_complexList(iRef_binary, canonical_rep="yes", include_generated_complexes="yes", list_methods="default")
-     #reconstructed_generated_ecoli_MITAB = convert_complexList_to_MITAB(generated_complexes_ecoli_complexList, irefindex_curr_ecoli, "yes", "yes")
-     #reconstructed_complexList = convert_MITAB_to_complexList(reconstructed_generated_ecoli_MITAB, canonical_rep="yes", include_generated_complexes="yes")
-     #setequal(dim(generated_complexes_ecoli_complexList), dim(reconstructed_complexList))
+     generated_complexes_ecoli_complexList = convert_MITAB_to_complexList(iRef_binary, canonical_rep="yes", include_generated_complexes="yes", list_methods="default")
+     reconstructed_generated_ecoli_MITAB = convert_complexList_to_MITAB(generated_complexes_ecoli_complexList, irefindex_curr_ecoli, "yes", "yes")
+     reconstructed_complexList = convert_MITAB_to_complexList(reconstructed_generated_ecoli_MITAB, canonical_rep="yes", include_generated_complexes="yes")
+     setequal(dim(generated_complexes_ecoli_complexList), dim(reconstructed_complexList))
 
-     #all_complexes_ecoli_complexList = convert_MITAB_to_complexList(irefindex_curr_ecoli, canonical_rep="yes", include_generated_complexes="yes", list_methods="default")
-     #reconstructed_all_ecoli_MITAB = convert_complexList_to_MITAB(all_complexes_ecoli_complexList, irefindex_curr_ecoli, "yes", "yes")
-     #reconstructed_all_complexList = convert_MITAB_to_complexList(reconstructed_all_ecoli_MITAB, canonical_rep="yes", include_generated_complexes="yes")
-     #setequal(dim(all_complexes_ecoli_complexList), dim(reconstructed_all_complexList))
+     all_complexes_ecoli_complexList = convert_MITAB_to_complexList(irefindex_curr_ecoli, canonical_rep="yes", include_generated_complexes="yes", list_methods="default")
+     reconstructed_all_ecoli_MITAB = convert_complexList_to_MITAB(all_complexes_ecoli_complexList, irefindex_curr_ecoli, "yes", "yes")
+     reconstructed_all_complexList = convert_MITAB_to_complexList(reconstructed_all_ecoli_MITAB, canonical_rep="yes", include_generated_complexes="yes")
+     setequal(dim(all_complexes_ecoli_complexList), dim(reconstructed_all_complexList))
+     }
      }
diff --git a/man/convert_edgeList_to_graph.Rd b/man/convert_edgeList_to_graph.Rd
@@ -54,7 +54,7 @@
 
      ## Additional info if you are using "igraph":
      V(graph_binary_INTACT)$name
-     V(graph_binary_INTACT)[degree(graph_binary_INTACT) == 1]$name
+     V(graph_binary_INTACT)[igraph::degree(graph_binary_INTACT) == 1]$name
      #par(mfrow=c(2,3))
      #plot(graph_binary_INTACT, layout=layout.fruchterman.reingold, vertex.size=3, vertex.color="green", frame=TRUE, main="Binary", vertex.label=NA)
      #plot(graph_complex_INTACT_s, layout=layout.fruchterman.reingold, vertex.size=3, vertex.color="green", frame=TRUE, main="Complex Spoke", vertex.label=NA)

diff --git a/man/create_id_conversion_table.Rd b/man/create_id_conversion_table.Rd
@@ -13,7 +13,7 @@ On iROGs and icROGs:
      }
      \arguments{
        \item{MITAB_table}{iRefIndex/MITAB R table.}
-       \item{data_folder}{Folder to save the text file: type "data" to save it in the "iRefR/data" directory, "home" to save it in the "R.home()" directory, or any other destination folder. Default = "data".}
+       \item{data_folder}{Folder to save the text file: type "data" to save it in the "iRefR/data" directory, "home" to save it in the "R.home()" directory, or any other destination folder. Default = getwd().}
        \item{output_filename}{File name for the conversion table files. Extensions ".txt" and ".RData" would be automatically added. Default="id_conversion_table"}
        \item{IDs_to_include}{Vector with the protein identifiers you want to convert from/to. iRefIndex iROGs and canonical iROGs are always included in the table. In addition, currently supports: UniProt ("uniprotkb"), RefSeq ("refseq"), GeneID ("entrezgene/locuslink"), Protein Data Bank ("PDB"), c("uniprotkb", "refseq", "entrezgene/locuslink") ("default") and all of them ("all"). Default = "default".}
      }

diff --git a/man/merge_complexes_lists.Rd b/man/merge_complexes_lists.Rd
@@ -18,6 +18,7 @@ The "complexList" format is one of the three table formats used by "iRefR", toge
      }
      \author{Antonio Mora <a.m.ortiz@biotek.uio.no>}
      \examples{
+     \dontrun{
      ## get tables
      irefindex_curr_ecoli = get_irefindex("562", "current", tempdir())
      iRef_binary = select_interaction_type("binary", irefindex_curr_ecoli)
@@ -29,3 +30,4 @@ The "complexList" format is one of the three table formats used by "iRefR", toge
      consolidated_complexList = merge_complexes_lists(list(complex_complexList, binary_complexList))
      number_complexes_repeated_inside_lists_or_between_lists = dim(complex_complexList)[1] + dim(binary_complexList)[1] - dim(consolidated_complexList)[1]
      }
+     }
diff --git a/man/select_protein.Rd b/man/select_protein.Rd
@@ -19,6 +19,7 @@
      }
      \author{Antonio Mora <a.m.ortiz@biotek.uio.no>}
      \examples{
+     \dontrun{
      ## get tables
      irefindex_80_mouse = get_irefindex("10090", "8.0", tempdir())
 
@@ -27,8 +28,8 @@
      output_2 = select_protein("icrogid", "4374882", irefindex_80_mouse, "not_full_complex")
      output_3 = select_protein("icrogid", "2892004", irefindex_80_mouse, "not_full_complex")
      output_4 = select_protein("icrogid", "2892004", irefindex_80_mouse, "full_complex")
-     #output_5 = select_protein("icrogid", "1365685", irefindex_80_mouse, "not_full_complex")
-     #output_6 = select_protein("icrogid", "1365685", irefindex_80_mouse, "full_complex")
+     output_5 = select_protein("icrogid", "1365685", irefindex_80_mouse, "not_full_complex")
+     output_6 = select_protein("icrogid", "1365685", irefindex_80_mouse, "full_complex")
 
      ## getting list of tables
      irog_list = c("1828087", "2892004", "1365685")
@@ -41,3 +42,4 @@
      irog_list = c("1828087", "2892004", "1365685")
      table_single = select_protein("irogid", irog_list, irefindex_80_mouse, "not_full_complex")
      }
+     }
diff --git a/man/summary_protein.Rd b/man/summary_protein.Rd
@@ -18,6 +18,7 @@
      }
      \author{Antonio Mora <a.m.ortiz@biotek.uio.no>}
      \examples{
+     \dontrun{
      ## get tables
      irefindex_80_mouse = get_irefindex("10090", "8.0", tempdir())
 
@@ -27,3 +28,4 @@
      output_3 = summary_protein("icrogid", "2892004", irefindex_80_mouse)
      output_4 = summary_protein("icrogid", "1365685", irefindex_80_mouse)
      }
+     }