Data set to predict autophagy induction in Podospora anserina

Description

This data set consists of all data files necessary to predict the putative interactions of the induction step of autophagy in Podospora anserina by means of the corresponding PPIs in human and yeast.

Usage

data("ai")

Format

human.ai.irefindex: Data frames with 1694 observations of 54 variables. yeast.ai.irefindex: Data frames with 3840 observations of 54 variables. pa2human.ai.homologs: Data frames with 261 observations of 12 variables. pa2yeast.ai.homologs: Data frames with 98 observations of 12 variables. human.ai.proteins: Named character vector with 5 elements. yeast.ai.proteins: Named character vector with 7 elements.

Details

Data frames human.ai.irefindex and yeast.ai.irefindex consists of all relevant interactions of the corresponding iRefIndex files. The two data frames pa2human.ai.homologs and pa2yeast.ai.homologs are the necessary parts of the result files from the BLAST searches of the P. anserina proteom against the proteoms of human and yeast. The named character vectors human.ai.proteins and yeast.ai.proteins consists of the proteins involved in the induction process of autophagy in human and yeast.

Value

Four data frames and two named character vectors (see above).

References

Camacho, C. et al. (2009). BLAST+: architecture and applications. BMC Bioinformatics, 10(1), 421.

Razick, S. et al. (2008). iRefIndex: a consolidated protein interaction database with provenance. BMC Bioinformatics, 9(1), 405.

Examples

data(ai)

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/ai.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ai
> ### Title: Data set to predict autophagy induction in _Podospora anserina_
> ### Aliases: ai human.ai.irefindex human.ai.proteins pa2human.ai.homologs
> ###   yeast.ai.irefindex yeast.ai.proteins pa2yeast.ai.homologs
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(ai)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>