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Last updated: 2021-12-06

Checks: 2 0

Knit directory: Tom_Proteomics/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

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R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Repository version: 452b6f2

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The results in this page were generated with repository version 452b6f2. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:

Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    analysis/figure/

Untracked files:
    Untracked:  analysis/preprocessing.Rmd
    Untracked:  data/27052020-TOTO-All-Clots-Sample-table.xls
    Untracked:  data/First 70 clots data for SAHMRI.csv
    Untracked:  data/First 70 clots data for SAHMRI.xlsx
    Untracked:  data/dge.rds
    Untracked:  data/modificationSpecificPeptides.txt
    Untracked:  data/peptides.txt
    Untracked:  data/proteinGroups.txt
    Untracked:  output/abundant_protein_heatmap.pdf
    Untracked:  output/variable_protein_heatmap.pdf

Unstaged changes:
    Modified:   analysis/_site.yml
    Deleted:    analysis/about.Rmd
    Deleted:    analysis/license.Rmd

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/index.Rmd) and HTML (docs/index.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
Rmd	452b6f2	Nhi Hin	2021-12-06	wflow_publish(c(“analysis/index.Rmd”, “analysis/import.Rmd”,
Rmd	389640b	Nhi Hin	2021-04-29	Start workflowr project.

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Motivation for this analysis

• This data describes protein abundance in different blood clot samples originating from patients (anonymised data). The data is fairly old and we are currently unsure what it actually looks like and whether there is value in the data. General exploratory and descriptive analysis needs to be done.
• Would like to know whether there are associations between particular metadata variables in samples that are associated with protein abundance measurements.

Analysis Steps

The analysis steps are summarised below.

1. Data import and cleaning: Protein abundances and sample metadata are imported, normalised, and filtered.
2. Basic data exploration: The following analyses were done to explore the data:

• Dimension reduction was used to see whether there is latent structure in the samples (e.g. whether clusters of samples exist).
• The most highly abundant and variable proteins were also pulled out to see whether there was biological significance/relevance in these.
• Correlation between sample metadata variables.
• Feature importance to determine whether sample metadata contributes to the protein abundances seen.

3. Building classifier / other analysis for statistical significance: Unfortunately the analysis cannot proceed to this step as there is a lack of significant association between the current metadata variables and protein abundance. Currently awaiting more samples - hopefully a larger sample size may help to reveal more subtle associations.