In rricepackage/rRice: rRice package to make easier the study of the genomic of rice

Informations about the vignette

In this vignette, you will find how to use the rRice package and it will be illustrated by examples. To use this package, you will have to create an experiment and then you will be able to work with it : Interrogate the databases Add manually databases * Create an array with specific genes and properties

Examples

1.) Create an experiment and add databases

The first thing you will have to do to use the package is to create a new experiment with the createExperiment(name, locus) function :

locus <- data.frame(ch = c("1"), st = c("148907"), end = c("248907"))
experiment <- createExperiment("newExperiment", locus)

Then you will have to follow instructions : First you will have to tell how many databases you want to experiment Then you will have to give the date of your experiment * Finally, you will have to choose which databases to choose

After succeeding these steps, you will have an operational experiment you will be able to use.

Example :

> locus <- data.frame(ch = c("1"), st = c("148907"), end = c("248907"))
> experiment <- createExperiment("newExperiment", locus)
How many databases do you want to experiment ? :1
Enter the date of the experiment (mm/dd/yyyy) : 09/17/2016
loading informations...
The list of the databases : 
1 for RAPDB 
2 for Gramene 
3 for Oryzabase 
4 for IC4R 
5 for Planttfdb 
6 for PLNTFDB 
7 for Funricigenes 
8 for Funricigenes2 
9 for Funricigenes3 
10 for MSU7 
1

Then wait for few seconds that your RAPDB database has been well-added to your experiment

2.) Consult your experiment

If you want to collect the informations about your experiment : name : experiment@name date : experiment@date databases : experiment@databases will return all the databases you have add to your experiment genes : experiment@genes will return the list of the genes of all the databases you interrogated properties : experiment@properties will return the list of the properties you selected with selectProperties(...) others : experiment@others will contain a list with your personal informations you added with the function addAttribute(...)

Example :

> experiment@name
[1] "newExperiment"
> experiment@databases
[[1]]
[1] "RAPDB"

3.) Add new databases to the experiment

If you wish to add new databases in your variable experiment :

experiment <- addDBs(experiment)

Then you will have to select the number of databases you want to add to your experiment and to choose which database to interrogate.

Example :

> experiment <- addDBs(experiment)
How many databases do you want to experiment ? :1
The list of the databases : 
1 for RAPDB 
2 for Gramene 
3 for Oryzabase 
4 for IC4R 
5 for Planttfdb 
6 for PLNTFDB 
7 for Funricigenes 
8 for Funricigenes2 
9 for Funricigenes3 
10 for MSU7 
2
loading informations of the database...

Then wait for few seconds that your RAPDB database has been well-added behind your preexisting databases Notice that your number of databases of your experiment has been modified :

> experiment@databases
[[1]]
[1] "RAPDB"

[[2]]
[1] "Gramene"

4.) Add manually a new database to the experiment

If you have a personal database you would like to integrate to your variable experiment :

experiment <- createNewDB(experiment)

Then you will have to give few informations about your new database you want to integrate in your experiment : Name of the new database The type if id of the first column of the file you want to import (rapdb or msu) The separator which is used in the file to separate every datas The path toward the file you want to import

Example :

> experiment <- createNewDB(experiment)
Your file has to be built as follow : 
First line is composed with all the names of the attributes
Others lines composed with all the values of the genes
Write the name of your new db :newDB
What kind of typeID is on the first row of your file (1 : msu; 2 : rapdb) : 2
Which separator is used in your file ? :,
Write the absolute path until your file :/path/towards/my/file.txt

Then the new database newDB has been well-added to your experiment variable and you will find all the genes you added in experiment@genes

5.) Others useful functions

a.) addAttribute function

If you want to add personal informations for your experiment then use this functions as follows :

> experiment <- addAttribute(experiment, "newAttribut", "1")
> experiment@others
[[1]]
newAttribut 
        "1" 

b.) Create an array with specific genes and properties selected by the user

After you added a lot of databases in your variable experiment, you may want to create an array with only few genes and few properties. To do so, you will have to :

1.) selectProperties function

The goal of this function is to select only the properties of your differents databases of your experiment you want to study :

> experiment <- selectProperties(experiment, list("RAPDB.id", "Gramene.geneIdx", "Gene.attribut1"))
> experiment@properties
[[1]]
[1] "RAPDB.id"

[[2]]
[1] "Gramene.geneIdx"

[[3]]
[1] "Gene.attribut1"

2.) selectGenes function

The goal of this function is to select only the genes of your databases of your experiment you want to study. The first argument of your function selectGenes is the experiment, the second is the list of genes you want to study listeGenes (rapdb or msu) and the last refer the type of id genes there are in listeGenes.

Example :

> listeGenes <- list("Os01g0104600","Os01g0104400")
> experiment <- selectGenes(experiment, listeGenes, "RAPDB")

3.) getProperties function

Thanks to 1.) and 2.) we will be able to create an array only with the genes and properties selected above. The first argument of the getProperties function is your variable experiment and the second represents which id of the gene will be present in the array (rapdb or msu).

Example :

> getProperties(experiment, "RAPDB")
                     rapdb.id gramene.geneidx gene.attribut1
Os01g0104400 OsNippo01g013050              72             12
Os01g0104600 OsNippo01g013200              75             14

rricepackage/rRice documentation built on May 24, 2019, 2:53 p.m.