Week 1

Question 1

argument

Answer 1

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

Question 2

bash

Answer 2

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

Question 3

bioinformatics

Answer 3

the science of collecting and analysing complex biological data.

Question 4

command

Answer 4

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

Question 5

CRAN

Answer 5

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

Question 6

csv file

Answer 6

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

Question 7

data frame

Answer 7

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

Question 8

exit status/code

Answer 8

value returned by a command or process to it’s caller.

Question 9

function

Answer 9

a set of statements allowing to perform a task

Question 10

getwd()

Answer 10

get your current working directory in R

Question 11

GUI

Answer 11

a graphical user interface through which users interact with electronic devices

Question 12

help() or ?

Answer 12

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

Question 13

install.packages()

Answer 13

install new R packages

Question 14

kernel

Answer 14

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

Question 15

library()

Answer 15

load a package that has been previously installed

Question 16

list

Answer 16

a set of objects of any class, linked together

Question 17

loop

Answer 17

process by which code can be repeated multiple times.

Question 18

MLST

Answer 18

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

Question 19

mode

Answer 19

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

Question 20

object

Answer 20

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…)

Question 21

package

Answer 21

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

Question 22

QC

Answer 22

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

Question 23

script

Answer 23

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

Question 24

setwd()

Answer 24

set your working directory

Question 25

shell

Answer 25

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

Question 26

string

Answer 26

a one dimensional array of characters

Question 27

terminal

Answer 27

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

Question 28

text editor

Answer 28

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

Question 29

text file

Answer 29

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…)

Question 30

UNIX

Answer 30

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

Question 31

user

Answer 31

the individual accessing system resources.

Question 32

variable

Answer 32

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

Question 33

vector

Answer 33

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