rncbi's Introduction

#Introduction With this package it is possible to access data from the NCBI Webservice inside R and use this data for further processing. The package provides the returned data in the form of a list object. This list can be inspected further, see the Examples for more details.

Installation

Installation of the package is quite easy as it doesn't need to compile anything. The only precondition is to provide Java 5 or higher.
To successfully install the RNCBI package the following packages are necessary.

rJava

To install this package, simply type

install.packages("rJava")

into the R console. Further informations on this package can be found at the rJava site.

If you are on a unix system, make sure R was configured with Java support.

To do this without re-installing R do

R CMD javareconf

on the command line, maybe root privileges are required to do this.

XML

This also can be installed with the package system from R, simply type

install.packages("XML")

Further informations can be found on http://cran.r-project.org/web/packages/XML/index.html.

RNCBI

The package itself can be installed from http://cran.r-project.org/ directly. To do this inside R type:

install.packages("RNCBI")

rncbi's People

Contributors

rncbi's Issues

Better Error reporting in NCBIRequestMethods

If a request will be set with an empty value argument, then the error says
that the parameter was not found. 

Instead it should report that the argument was empty or not initialized.
The method "setRequestParameter" should distinguish between missing value
and wrong parameter.

Original issue reported on code.google.com by Martin.Schumann.email on 5 Jun 2010 at 12:11

Connecting to protein database with EFetch

What steps will reproduce the problem?
1. EFetch(ncbi, "protein")

What is the expected output? What do you see instead?
Creation of EFetch object for 'protein' database results in an error. It is 
possible to connect to this protein via the web browser, though.

What version of the product are you using? On what operating system?
RNCBI_0.9.1 on R 3.0.2

Please provide any additional information below.
The following query works in the browser, connecting to the "protein" database:
 http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=protein&id=15718761&rettype=ft

Yet, providing "protein" as a dabatase to EFetch results in the following error:

[ERROR] Error occured: 
de.hzi.infg.exceptions.ErrorFromWebserviceExeption: Wrong database selected. 
Please select one from these databases:
pubmed, nlmc, taxon, omim, snp, sequence, journals, gene
    at de.hzi.infg.RequestEFetch.<init>(RequestEFetch.java:98)
    at de.hzi.infg.RInterface.initEFetchOperation(RInterface.java:503)
An object of class "EFetchClass"
Slot "NCBIObj":
An object of class "NCBIClass"
Slot "interface":
[1] "Java-Object{de.hzi.infg.RInterface@162200d5}"

Original issue reported on code.google.com by [email protected] on 10 Oct 2013 at 6:17

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