Major method of the Path2PPI class to predict the final PPI in the
target species using the information available from the stored reference
species. Different values for the arguments of this method can lead to
different PPI networks, differing in the degree of reliability and strictness.
Which interaction from the reference species should be taken into account.
"both": both interactors of an interaction has to be in the initial protein
list previously inserted by the user (recommended if it is a large network or
many proteins were initially defined, respectively). "one": only one of the
interactors of each reference interaction has to be in the initial protein
list (may lead to very large networks).
h.thresh
E-value cutoff at which each homologous relationship definitely will be
declined (see also h.range argument).
h.range
Numeric vector consisting of two values. The first value indicates the lower
border (smallest E-value). Each E-value which is equal or less than this
border is scored with 1 (best). The second value indicates the upper border
(biggest E-value). Each E-value which is equal or greater than this border is
scored with 0 (worst).
i.thresh
Numeric. Threshold for accepted interactions. If the computed prediction score
for an interaction is less than i.thresh it will be declined.
consider.complexes
Logical. If TRUE then interactions are also considered which actually
indicate an association of the current protein to one bigger protein complex.
This may lead to very large networks if mode="one" since all other
proteins of this complex are considered as well, i.e., each protein in such
complexes are considered to interact with each other protein of this complex.
If mode="both" then each protein of an complex has to be in the initial
protein list to consider each interaction (see details).
max.complex.size
Numeric. Is only considered if consider.complexes=TRUE. The maximum
size of complexes to be considered.
decline.self.interaction.ref
Logical. If TRUE then all self interactions from reference species are
declined.
decline.self.interaction.tar
Logical. If TRUE then all predicted self interactions in target species
are declined.
verbose
Logical. FALSE hides messages in the output.
Details
Difference of h.thresh and h.range: If only one protein in the
target species was found to be homologous to a current reference species
protein and this homology was rated with an E-value which is equal or smaller
than h.thresh it is scored with 1 (even if the E-value is larger than
the upper border of h.range). See package vignette for more details.
Use the complex arguments with care, since each complex may lead to a vast
amount of interactions, i.e., each protein is considered to interact with each
other of this complex; e.g. if there are 10 proteins involved in one complex,
this would lead to 10 over 2 = 45 interactions.
Value
An object of the class Path2PPI with predicted PPI.
data(ai) #Load test data set
ppi <- Path2PPI("Autophagy induction", "Podospora anserina", "5145")
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)
#Using the default settings leads to 8 predicted interactions in the
#target species
ppi <- predictPPI(ppi)
#Consider complexes where each complex is allowed to be up to 10 proteins
#large. For this smaller pathway only one more interaction was predicted when
#considering larger complexes.
ppi <- predictPPI(ppi,consider.complexes=TRUE,max.complex.size=10)
#We can be less strict and decrease h.range what obviously increases the
#number of predicted interactions to 13
ppi <- predictPPI(ppi,h.range=c(1e-60,1e-20))
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)
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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/predictPPI.Rd_%03d_medium.png", width=480, height=480)
> ### Name: predictPPI
> ### Title: Prediction of the PPI
> ### Aliases: predictPPI
>
> ### ** Examples
>
> data(ai) #Load test data set
>
> ppi <- Path2PPI("Autophagy induction", "Podospora anserina", "5145")
> 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.
>
> #Using the default settings leads to 8 predicted interactions in the
> #target species
> ppi <- predictPPI(ppi)
Begin with Homo sapiens
6 interactions processed. These lead to 0 interactions in target species.
-------------------------------
Begin with Saccharomyces cerevisiae (S288c)
15 interactions processed. These lead to 8 interactions in target species.
-------------------------------
Combine results to one single PPI.
A total of 8 putative interactions were predicted in target species.
>
> #Consider complexes where each complex is allowed to be up to 10 proteins
> #large. For this smaller pathway only one more interaction was predicted when
> #considering larger complexes.
> ppi <- predictPPI(ppi,consider.complexes=TRUE,max.complex.size=10)
Begin with Homo sapiens
9 interactions processed. These lead to 0 interactions in target species.
-------------------------------
Begin with Saccharomyces cerevisiae (S288c)
24 interactions processed. These lead to 17 interactions in target species.
-------------------------------
Combine results to one single PPI.
A total of 9 putative interactions were predicted in target species.
>
> #We can be less strict and decrease h.range what obviously increases the
> #number of predicted interactions to 13
> ppi <- predictPPI(ppi,h.range=c(1e-60,1e-20))
Begin with Homo sapiens
6 interactions processed. These lead to 5 interactions in target species.
-------------------------------
Begin with Saccharomyces cerevisiae (S288c)
15 interactions processed. These lead to 22 interactions in target species.
-------------------------------
Combine results to one single PPI.
A total of 13 putative interactions were predicted in target species.
>
>
>
>
>
> dev.off()
null device
1
>