Simple try-catch code in R

Here is a simple code sample to demonstrate tryCatch function in R.

x <- tryCatch( "OK", 
          warning=function(w){     
            return(paste( "Warning:", conditionMessage(w)));
          }, 
          error = function(e) {      
            return(paste( "Error:", conditionMessage(e)));
          }, 
          finally={
            print("This is try-catch test. check the output.")
          });
print(x);

x <- tryCatch( warning("got a warning!"), 
               warning=function(w){     
                 return(paste( "Warning:", conditionMessage(w)));
               }, 
               error = function(e) {      
                 return(paste( "Error:", conditionMessage(e)));
               }, 
               finally={
                 print("This is try-catch test. check the output.")
               });
print(x);


x <- tryCatch( stop("an error occured!"), 
               warning=function(w){     
                 return(paste( "Warning:", conditionMessage(w)));
               }, 
               error = function(e) {      
                 return(paste( "Error:", conditionMessage(e)));
               }, 
               finally={
                 print("This is try-catch test. check the output.")
               });
print(x); 

How to change the limit of uploaded file size in php?

Edit the following configurations in the php.ini file, and then restart webserver (apache).

upload_max_filesize = 10M
post_max_size = 20M

You may find the php.ini file in /etc/php5/apache2 directory of ubuntu. If you forget the location of ini file, you may find it by running a simple php file as below.

<?php
   phpinfo();
?>

Note: you will probably require write permission to edit the php.ini file.

For more information, you may visit this page. 

Automatic mapping (or conversion) among different biological databases

biomaRt is an R package to map among different biological databases. Here is a simple code-snippet to convert human gene id to gene symbol.

library(biomaRt)
ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl")
symbols = getBM(attributes=c('entrezgene','hgnc_symbol'), filters='entrezgene', values=c("7157","5601"), mart=ensembl) 

Installation note:

• In Ubuntu, you may need to install 'libxml2-dev' and 'libcurl4-openssl-dev'.