I have a really (long time) important question here, and I will really appreciate any help
I'd like to perform several statistical tasks using R environment under unix system. Actually up to now I have used R Studio (windows), for ecology studies, but now I have huge tables of metagenomic data to analyze.
I created my Mysql database (unix) of metagenomic data, with reads and uniprot's and Knumbers and taxid's and so so so on. This means that I have dozens of tables with thousands (even millions) entries. Now I have to perform some tasks unavailable on Mysql functions, like variance analysis, PCA, cluster, regression, even stepwise model choices.
I have tried to install the RMySQL and dbConnect packages on R Studio, but I got the message:
Warning in install.packages : package 'dbConnect' is not available (for R version 3.1.0)
I searched for this error and none of the available suggestions and comments and possible solutions worked to me.
Besides of this, what would be really efficient would be do this connection between R and Mysql under command line unix system.
My R version on unix is
R version 3.1.0 (2014-04-10) -- "Spring Dance" Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-redhat-linux-gnu (64-bit)
My MySQL version is:
Welcome to the MySQL monitor. Commands end with ; or \g. Your MySQL connection id is 1081 #----> I think that this id will be important, right? Server version: 5.1.73 Source distribution
I don't know what to do, I searched for this in many blogs, forums, I asked my colleagues and advisors, no one around me could help me, for now.
You can just send to me links and any kind of material (books, tutorials), I can try to do this by myself, but I need, at least, a objective reading about this (or someone that did this).... I have dozens of R books and tutorials and none of them help to do this.