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EpiCompBio / genotype_QC_lite

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Getting QC reports #1

Open davidmosen opened 7 years ago

davidmosen commented 7 years ago

We need to take a look at aw_stats.r and update it to get more stats. We can integrate those with the generated plots to create a report.

antoniojbt commented 7 years ago

What's the purpose of the script? It looks like it currently puts together a list of included and excluded individuals?

Are we looking for relatively simple marker and individuals stats? If so we could reformat/save/rename plink's logs and run it's summary statistics commands.

davidmosen commented 7 years ago

I'm working on something a bit more comprehensive and polished. Will share it soon and we can brainstorm what else would be needed for a barebone report.

antoniojbt commented 7 years ago

Sounds good!

davidmosen commented 7 years ago

Please see "/groupvol/med-bio/epiUKB/Airwave/QC/affy_b37_maf0.01/report/"

You will need to download the folder and then open the file called "report.html" to view it properly.

antoniojbt commented 7 years ago

I had a quick scan, looks excellent! I didn't check the actual results, we should meet/email to discuss these separately.

I haven't seen how you generated it. Is it easy to transfer to other planned pipelines? Easy to learn? Thanks!

davidmosen commented 7 years ago

Antonio, the report is generated by lines 90-93 in file aw_all_batches.sh:

cd ${PBS_O_WORKDIR}
cp -r assets ${OUTPATH}/report/
Rscript -e "library(knitr); knit('report.Rhtml', output='${OUTPATH}/report/report.html')" $PARAMS

The core code is in report.Rhtml, which works just like Sweave or the markdown for plain text that you were using, with the only difference that this mixes R with HTML, rather than LaTeX or plain text. The background HTML+CSS+JS design can be applied to other pipelines/reports for sure.