A character string giving the taxonomy identifier.
proteins
Either a character vector with the identifiers of the proteins which are
involved in the corresponding pathway or a character vector with the protein
names or aliases, respectively, named by the protein identifiers.
irefindex
Either a data frame, representing the iRefIndex table of the current reference
species, e.g. loaded previously via read.table, or the corresponding
file name of the iRefIndex file.
homologs
Either a data frame representing the results of the BLAST search (e.g. loaded
previously via read.table) or the corresponding file name of the BLAST
result file.
Details
This method searches for all relevant interactions in the data frame or file
defined in iRefIndex. There are different and often ambiguous protein
identifiers defined in an iRefIndex file, and the putative "major" identifiers
are not necessarily those defined in the corresponding "major" columns "uidA"
and "uidB". Furthermore, iRefIndex also contains protein complexes. Hence,
Path2PPI applies an advanced search algorithm to automatically find
relevant interactions associated with the pathway or the proteins of interest,
respectively. The user does not have to predefine the identifiers types
(Uniprot, Swissprot, Ensemble etc.), since these types are often unambiguously
assigned. The algorithm searches for each identifier in 10 columns where any
type of identifier or accession number is defined ("uidA", "altA",
"OriginalReferenceA", "FinalReferenceA", "aliasA", "uidB", "altB",
"OriginalReferenceB", "FinalReferenceB" and "aliasB"). Additionally, it
searches for each complex which contains one or more of the predefined
proteins. Subsequently, each homologous relationship which is not relevant for
the previously found interactions is declined. The results of these searches
are centralized in the Path2PPI object and can be visualized using the
appropriate methods (e.g. showReferences)
Value
An object from the class Path2PPI with attached reference species.
data(ai) #Load test data set
ppi <- Path2PPI("Autophagy induction", "Podospora anserina", "5145")
ppi
ppi <- addReference(ppi, "Homo sapiens", "9606", human.ai.proteins,
human.ai.irefindex, pa2human.ai.homologs)
ppi <- addReference(ppi, "Saccharomyces cerevisiae (S288c)", "559292",
yeast.ai.proteins, yeast.ai.irefindex,
pa2yeast.ai.homologs)
ppi
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(Path2PPI)
Loading required package: igraph
Attaching package: 'igraph'
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Path2PPI/addReference.Rd_%03d_medium.png", width=480, height=480)
> ### Name: addReference
> ### Title: Add reference species
> ### Aliases: addReference
>
> ### ** Examples
>
> data(ai) #Load test data set
>
> ppi <- Path2PPI("Autophagy induction", "Podospora anserina", "5145")
> ppi
Autophagy induction in Podospora anserina (5145)
-------------------------------------------------
No reference species yet.
-------------------------------------------------
No predicted PPI yet.
>
> ppi <- addReference(ppi, "Homo sapiens", "9606", human.ai.proteins,
+ human.ai.irefindex, pa2human.ai.homologs)
Search for all relevant interactions:
0%--25%--50%--75%--100%
Remove irrelevant homologs.
> ppi <- addReference(ppi, "Saccharomyces cerevisiae (S288c)", "559292",
+ yeast.ai.proteins, yeast.ai.irefindex,
+ pa2yeast.ai.homologs)
Search for all relevant interactions:
0%--25%--50%--75%--100%
Remove irrelevant homologs.
> ppi
Autophagy induction in Podospora anserina (5145)
-------------------------------------------------
2 reference species: 9606, 559292
-------------------------------------------------
No predicted PPI yet.
>
>
>
>
>
> dev.off()
null device
1
>