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Writing and Reading Sequence Data in R




Installing R on Personal computers



  1. Go to http://ftp.heanet.ie/mirrors/cran.r-project.org.
  2.  Download R for Linus/ Mac OS X/windows
  3. To install R on Macintosh or computer running Linux chose specific R installer http://ftp.heanet.ie/mirrors/cran.r-project.org and follow the instructions provided to complete installation process.
  4. After completing installation, check the R icon on the desktop.
  5. Or else From Start button, chose All programs and start R from the menu bar.
  6. The R console will pop-up in the user computer interface.
  7. R has some standard packages installed, moreover additional R packages such as “rmeta” package can also be installed by the user-end.
  8.  “Install package(s)” needed by the user from the “Packages” menu at the top of the R console.
  9. Bioconductor packages, additional R packages for bioinformatics, can be installed from http://bioconductor.org/biocLite.R


Running R in personal computer


  • User can provide R commands into the R console for programming.


This represents an R prompt, then type commands for a task to be performed and the results will be tabulated immediately.

  • Objects are variables either scalars, vectors arrays, data frames, tables, lists and matrices created in R. Arrow represents values assigned to a particular variable.

        Example of a scalar variable :  > x <- 2*3

  • View the contents on R object by typing its name >x
  •  Example of a vector variable: Use the c()(combine)function to create a vector.
  • Suppose if the user is creating a vector named myvector, give the values of the elements as follows: > myvector <- c(7, 5, 8, 11, 4)
  • Type myvector to see the contents of the variable.

       > myvector [1] 7, 5, 8, 11, 4, where the number in the square bracket represents the index of the element. If the user need to  extract 2 element of the variable, type as > myvector[2]

  • List contain both numeric and character elements. It can also include variables as vectors. Create mylist as > mylist <- list(name="John", wife="Julie", myvector)
  • Print the contents of the list mylist by typing its name as

                   > mylist $name [1] "John"
                   $wife [1] "Julie"
                  [1] 7, 5 ,8 ,11 ,4

  • For table variable, first  create a vector variable mynames containing the name, for example the name of members in a family. Use table function table() function to read the names in the table list

              > mynames <- c("Mary", "John", "Ann", "Sinead", "Joe", "Mary", "Jim", "John",
               , →"Simon") > table(mynames)
                   Ann Jim Joe John Mary Simon Sinead
                    1 1 1 2 2 1 1

  • User can store the table variable produced by the function table(), and call the stored table “mytable”, by following the command > mytable <- table(mynames)
  • Using the attributes() function, user can find out the names of the named elements in a list.

             > attributes(mylist)
            [1] "name" "wife" ""

  • Arguments, which are input variables can be provided to carry out mathematical operations.

        > log10(1000)

  • help() function will provide the user  information about the function to be calculated.

            > help.search("deviation")

  • function sd() in the “stats” package, which available with R installation, calculates  the standard deviation.
  • RSiteSearch()function provide the basic information of all the functions described on the R website.
  • To calculate the average of myvector, follow > mean(myvector)
  • Uisng the basic knowledge on R programming, user can create functions for calculating complex mathematical operations also.
  • Follow, > q() to quit from R interface.



Procedure to Work Simulator


  1. A default.CSV/FASTA file is available on the R platform.
  2. User can choose their required sequence and can load the sequence.fasta file/sequence.csv file into the platform
  3. Follow the code in the command window:

              dnaseq <- read.csv("sequence.fasta")

    4. Click Execute Button for output.  


Description: The common functions, “read.csv” and “write.csv”. are using in R programing for reading and writing coma separated files. Here, we are also using these functions for reading and writing our sequence files. This is not a systematic way of accessing sequence file like FASTA and genbank, in R programing. Using the read.csv function, user can read the sequence data in a file and assign to a variable named “dnaseq”. With the function write.csv, user can write a sequence data into a sequence file.




Cite this Simulator:

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