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In the ‘2.Setup’ section, you downloaded 3 nfcore/sarek runs to H:/workshop/sarek/runs. These represent sarek variant calling results from the 3 exercises run in session 2:

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SNPeff creates its own variant analysis reports (html reports) for each sample, which can be seen here:

H:/workshop/sarek/runs/run2_trio/results/reports/snpeff/haplotypecaller

We’ll be creating our of reports, with some additional functional information, using R.

R Markdown

We’ll be running

In RStudio

Go to:

creating html reports using R Markdown. These reports contain ‘chunks’ of R code and markdown language, which allows text, headings, etc to be added to a report.

https://rmarkdown.rstudio.com/

As an example, in RStudio, select

‘File’ → “New File” → “R markdown”

Then click ‘OK’

This will create a basic example markdown report.

Click ‘Knit’ to generate the report. It will ask you to name the file and ask where to save the file. Call it ‘test’ and save it in H:/workshop

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You will see it generates the test html report.

Functional analysis

For our report we will be taking the SNPeff results and seeing if the list of variants, and the genes associated with them, are overrepresented in metabolic pathways.

To do this we will use the R clusterProfiler package, which examines enrichment of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and Gene Ontology (GO) terms, based on a set of input genes. In this case, the genes associated with the SNPeff variants.

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Initial setup

The R script and R Markdown scripts have already been created, so you’ll just need to open them in RStudio.

In RStudio, select ‘File’ → “Open File”

Browse to H:/workshop/sarek/runs/run2_trioSetup

Select the ‘modify.R’ file and click ‘Open’.

Open the ‘function_report.Rmd’ file in the same way (it’s in the same location as modify.R)

These are the two files you’ll need to generate the reports.

G:\Other computers\Home PC\Desktop\QUT\Liver_exome_variants\sarek

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