Glossary

Glossary of less known terms used in this course

argument – generally, arguments are options controlling how functions and commands should operate on specific data

bash – Bourne Again Shell (Bash). A shell developed by Brian Fox in 1988.

bioinformatics – the science of collecting and analysing complex biological data.

command – a type of input, typically given in a terminal, which instructs the system to perform a given task.

CRAN – the Comprehensive R Archive Network. Provides access to mirrors, a set of sites spread worldwide, for downloading R and related packages

csv file – comma-separated values file. In these files, a “comma” delimiter is used to separate items of the same line

.csv – extension of a csv file

data frame – a group of vectors organised together in a list. In other words, a data frame is a data set containing data organized in columns and rows

exit status/code – value returned by a command or process to it’s caller.

function – a set of statements allowing to perform a task

getwd() – get your current working directory in R

GUI – a graphical user interface through which users interact with electronic devices

help() or ? – help() is a function and “?” an operator in R to provide help

install.packages() – install new R packages

kernel – the computer program at the core of an operating system. The kernel has control of everything in the system

library() – load a package that has been previously installed

list – a set of objects of any class, linked together

loop – process by which code can be repeated multiple times.

MLST – multilocus sequence typing. A technique in microbiology for isolating microbial species using the DNA sequences of housekeeping genes.

mode – the property of an object in R, such as numeric, character, logical, etc…

object – a variable or a data set or any form of item containing information created or used in R. More generally, anything that has a “mode” is an object in R (data frames, vectors, lists, etc…)

package – a collection of functions and commands written in order to achieve a certain goal in R, and allowing users to easily query their data using specific commands and arguments for each package

QC – quality control. In DNA sequencing, ensuring that the sequenced data is suitable to use in further analyses.

script – a form of computer program, typically a file, which contains a collection of commands.

setwd() – set your working directory

shell – generic name for an application or program which provides access to the underlying system resources.

string – a one dimensional array of characters

terminal – a GUI-based interface into which users can type commands and print text output

text editor – a computer program for editing plain text files. This differs from a word processor, which includes text formatting.

text file – a computer file in which data is stored in a particular structure of successive lines. When used for more complex purposes, it is generally structured in lines for the entries and in columns or “fields” for different conditions. All elements in these entries are delimited from one another by “separators” (spaces, tabulation, etc…)

UNIX – is an operating system developed by Bell Laboratories of AT&T, and is an example of a multi-tasking, multi-user operating system

user – the individual accessing system resources.

variable

• a string of characters that is used to denote some value stored within the computer and may be changed during execution of a programme
• an object in R that stores data in a specified manner, and can be used to easily manipulate the data

vector – the simplest structure of data in R, consisting of elements called components