Do correlations between any three pairs of variables using the cor.test function

3.2. Basic Numerical Descriptions
5. Basic Plots
12. Case Study: Working Through a HW Problem
The Commands:
(1) Run the following commands on RTestData.txt
(2) For each question, copy and paste both the code and the output, including graphs, after each number (starting with reading in the file to a dataframe from your computer.)
(3) You can copy and paste the questions and the answers right into the document.
———————————————————-
1) Mean, median and standard deviation for any three bacteria.
2) Histograms of any two species.
3) Boxplots of any two species.
4) QQplots: qqline plot of veil
5) QQline plot of square root transformation of of the veil data Hint: x=sqrt(d$veil)
6) Two plots of one bacteria verses another Hint: plot(d$strep,d$fuso)
7) Add a line to the plots with lm
>m = lm(d$fuso ~ d$pocket, data=d)
>abline(m)
8) Do correlations between any three pairs of variables using the cor.test function – cor.test(d$strep,d$fuso)
Part II

Linux/Unix exercise (Linux is the open source version of the UNIX operating system)
For this assignment, you will need a UNIX shell environment. A Linux/Unix Computer, the Mac OS is a Linux/Unix environment, or

you try and find an online version. There is also a BASH terminal for Windows 10.
Assignment:
Use Chapter 8 of Computational Biology and this online tutorial to perform all the commands below. http://www.ee.surrey.ac.uk/Teaching/Unix/
Commands to Run:
(1) Run the commands in the Unix basics tutorial on the website. https://kelleybioinfo.org/algorithms/basics/index….
(2) Run the commands (as many as you can) in the first 4 tutorials of: http://www.ee.surrey.ac.uk/Teaching/Unix/
(3) To run the commands in Tutorial 2 you will need a file called science.txt. To make this file run the following:
% echo “my data: ACTGTTTGC” > science.txt

id strep prev lepto fuso veil time status pocket deepest
S001 57.4 10.2 0.1 0 6.9 1 2 2.7 3.8
S001 26 0 25.6 0 6.3 2 2 2.7 3
S006 19 24.2 4.8 5.7 4.2 1 1 2.5 3.2
S006 15.2 4.2 0.2 2.6 3.4 2 1 2.4 3.2
S007 33.2 2.3 7.4 1.3 12 1 2 2.4 2.7
S007 18 0.3 13.6 1.7 13.8 2 2 2.4 2.8
S008 12.3 11.5 9.1 5.5 5.7 1 1 2.6 3.5
S008 3.3 24.7 6.3 10.4 3 2 1 2.5 3.2
S009 9.1 32.7 1.9 14.3 1.6 1 1 2.9 4
S009 22 8.9 17.8 4.8 14 2 1 2.5 3.5
S012 11 17.5 8.9 3.4 4 1 0 1.6 2
S012 1.8 11.7 29.1 8.4 3.7 2 0 2.5 2.7
S013 4.8 10.6 3.7 10.5 1 1 0 2.4 3.3
S013 6.6 3.4 13.9 9 4.1 2 0 2.6 3.5
S015 9.1 19.5 14.3 6.7 16.9 1 1 2.6 3.7
S015 9.7 7.3 14.7 6.2 22.8 2 1 2.1 2.8
S016 18.1 9.6 5.6 6.7 7.9 1 2 2.7 3.5
S016 8.8 8.3 6 8.1 4.9 2 2 2.7 3.5
S019 14.2 10.4 9 11.8 4.9 1 1 2.7 3.8
S019 8.1 3.1 11.2 25 3.8 2 1 2.6 3.7
S020 8.8 10.7 17.4 5.1 1.7 1 1 2.5 3
S020 24.1 7.7 10.8 5.8 11.8 2 1 2.4 2.7
S022 3.6 27.4 9.6 9.3 1.6 1 1 2.5 3.2
S022 9 9.6 16.3 8.3 2.3 2 1 2.4 2.7
S023 9 35 3.2 7.6 3.4 1 2 3.2 5.2
S023 3.1 22 13.1 6.7 4.8 2 2 3.2 4.8
S024 5.1 9.2 4.9 10.5 1.3 1 1 3 4.2
S024 23.3 7.6 18.7 9.1 5.2 2 1 2.7 3.7
S025 12.2 0.3 2.8 1.4 0.6 1 0 2.5 2.8
S025 3.3 0.5 2 5.7 0.1 2 0 2.9 3
S032 11.4 15.7 18.6 6.6 3.6 1 0 1.6 2.2
S032 5.3 14.1 15 17.1 4.7 2 0 2 2.8
S033 10.7 18.8 10.2 7.5 9 1 0 1.3 2
S033 8.5 17 17.7 8.7 3.5 2 0 2.7 4
S035 10.1 39.9 4.4 7.1 4.1 1 1 3 3.8
S035 6.2 26.2 13.3 6.4 2.1 2 1 2.5 3.3
S038 9.2 12.4 3.5 11.5 11.5 1 0 2.5 3.8
S038 5 11.5 5.8 17.8 5.3 2 0 3 4.2
S039 3.9 14.2 13.8 18.5 1.9 1 0 3.1 4
S039 11.4 11.7 9.3 7.5 11.7 2 0 3.2 4.5
S040 18.6 2.4 10.3 8.8 6.4 1 1 2.7 3.7
S040 5 16.9 4.4 15.4 4.7 2 1 2.6 3.3
S043 61.7 1.7 0.4 2.6 2.4 1 2 2.5 3.3
S043 4.3 19.4 3.5 9.1 1.9 2 2 2.5 3.2
S045 16.1 6.9 9.9 10.1 3.1 1 2 2.9 4.2
S045 2.9 6.6 4.3 17.1 0.8 2 2 2.9 4.2
S049 0.9 6.6 3.2 7.1 6.7 1 1 3.8 4.3
S049 2.7 20.2 8.3 12.5 5.6 2 1 3.4 3.8
S051 6.6 10.9 11.7 9.7 5.4 1 0 2.3 3
S051 16.2 8 12.2 11.6 4.1 2 0 2.4 3.2
S052 2.9 3.1 26.6 9.3 9.8 1 0 1.6 1.8
S052 6.4 19.6 5.9 11.8 14.2 2 0 2.3 2.7
S055 10.7 7.6 15.1 12.3 3.8 1 0 2.7 3.7
S055 5.6 12.2 10.1 15 1.8 2 0 3 4.7
S056 6.1 13.9 3.6 23.8 0.8 1 0 2.8 4.2
S056 8.1 10.6 7.2 19.5 7.8 2 0 3.1 4.2
S057 19.1 10.4 9.6 7 9.3 1 0 1.9 2.3
S057 26.2 7.4 17.3 10.5 1.9 2 0 3.4 3.8
S058 22.1 11 11.9 11.8 4.4 1 0 2.6 2.3
S058 7.9 5.3 21 13.4 26.2 2 0 2.8 3.3
S060 4 29.9 18.9 3.2 4.1 1 0 2.5 3
S060 40.4 8 1.9 4.1 8.9 2 0 2.8 3.2
S061 36.5 1.9 10.8 4.9 10.8 1 1 2.7 2.5
S061 23 1.5 18.1 11.2 7.4 2 1 2.5 2.7
S062 39.8 0.7 7.6 0.3 4.5 1 0 2.3 3
S062 24 7.1 21.1 1.9 8.8 2 0 2.4 3
S063 19.9 0 2.5 0 0.1 1 0 2.5 2.8
S063 24.8 2.5 9.1 7 3.2 2 0 2.7 3.7
S065 7.1 12.3 2.5 11 5.1 1 0 2.4 3.7
S065 11.8 10.2 9 15.7 6.3 2 0 2.7 3.3
S068 15.9 23 9.8 6.7 7.3 1 0 2.2 3.7
S068 16.8 11.6 27.1 7.9 2.2 2 0 2.8 4.2