Data Description Group Task

Data description

The data for the Take Home Assessment, available under the Data Files folder in the Take Home Assessment section on Moodle, contain information of about 6000 cells in a biological experiment. You are given three files cell_data.csv, cell_data_additional.csv and donor_info.csv.1

  • In csv, each row stores relevant information for a cell and has five comma-separated values:
    • UID: this is the unique identifier for the cell.
    • X1and X2: these are two characteristic values of the cell. They are statistics summarising genetic information in each cell in two most informative numbers.2
    • CellType: this indicates whether the cell is a B cell (B) or a T cell (T). You don’t need to worry about the biology here – just treat them as two different categories of cells.
    • Donor: the identifier of the donor from whom the cell was taken.
  • In csvcontains information for some additional cells:
    • UID: this is the unique identifier for the cell.
    • X1and X2: these are two characteristic values of the cell, defined in the same way as in csv.
  • In csv, each row has three comma-separated values:
    • Donor: the identifier of the donor, they contain all the values in the Donorfield of the csv file (and some other donors not present in the cell_data.csv file).
    • Age: age of the donor, measured in years.
    • Gender: gender of the donor, Femaleor Male.

 Group component

In this group component, you will need to use cell_data.csv and donor_info.csv. As a group, you will describe and analyse all the data in these two files by answering the problems below. Your analysis must be based solely on the data given to you. Do not introduce other data into your work. Also, you do not need to investigate the source of the data further.

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3.1 Group Tasks

  1. Using techniques such as summary statistics and plots, describe the cell data in your report. Your description should include both univariate and multivariate analysis.

.2 What to submit

Please submit two files for your group component:

  1. A PDF report named pdf. The report should be consistent with the following:
    1. You must use the Microsoft Word template provided on the Moodle page for your report and not change its font, font sizes or margins. If the template has been changed, up to 4% of marks can be lost and I will reformat the document to the template standard, to which the following point will apply.
  • The report must be capable of being read on its own: i.e., it should not refer to the R program but just contain data/plots from the program’s output.
  • Please save your report as a PDF file from Microsoft Word (FILE, Export, Create PDF/XPS).
  • It must be written in clear comprehensible English with readable and well-labelled figures.

2.。An R program named analysis.R. Your R program should satisfy the following:

  • It should be clearly laid out and well commented.
  • You can assume that all data files are in the working directory, i.e., there should be no setwd()command or reference to directories.
  • It may use non-standard packages (remember to include a library()command to load them) and you can assume that they are installed on my computer.
  • It should create an output file named txt, containing only the statistics you use in your report. Your program may investigate other things but the output file should contain all the information you use in your report. The output file itself should notbe included in your submission. Instead, I will run your program using the source() function in R to generate your output file.
  • Create a .pdfimage file for each plot (or set of plots) that you use in your report, and no others. Name the image files pdf, fig2.pdf, …, following the same order in which they appear in your report. Do not submit the figures. They should be created when I use the source() function to run your program.

 

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