dahn-youngdong / finalproject Goto Github PK

https://github.com/dennisdong123/finalproject/blob/3c038207dcecd767e681501b31f33b7ce6c932c8/minimim_viable_analysis.Rmd#L84

What is the purpose of this block of code? Usually installation is handled separately from loading the packages. Were you able to get it to run?

https://github.com/dennisdong123/finalproject/blob/73247ca5ffe147d26a595a970145d460035a29e6/2.filter.Rmd#L12-L28

I am closely following https://github.com/jdalapicolla/LanGen_pipeline_version2
But my data after the filter show no data left. Why? how do it make the script work?

https://github.com/dennisdong123/finalproject/blob/cb8eb7771b2cc9b73764cacbca8cab0c78a99127/DahnYoung_Dong_Final.Rmd#L288-L293

Dear PhyloBio Team,

I am almost done with all analyses and pretty satisfied with the progress. Yet when I knit the markdown, it seems the visualization results differ every time? Why is it? I don't expect the result to change though because there is no random seed or permutations, etc...

Can you help? I don't know how to interpret the result now, because they seem to change every time. The colors should match the ancestry because I set the palette the same every time, didn't I?

From MVA document,

#Look at depth, quality, HWE, HE, allele frequencies, and Pi site.depth <- r2vcftools::Query(snps_unind, type="site-mean-depth") summary(site.depth$MEAN_DEPTH) #Mean = 3.59 / Median = 2, about 1/20 smaller than the example hist(site.depth$MEAN_DEPTH, breaks=200) quality <- Query(snps_unind, type="site-quality") summary(quality$QUAL) #all 13 with seemingly no variation hist(quality$QUAL) ## something wrong here.

I included in the output folder the Robject- "snps_unind", which should allow you to run the code from line 200.

Does it suggests anything wrong with my data quality?

Best,

https://github.com/dennisdong123/finalproject/blob/fc9d6df1e9b41a3f0adcd509fe42a64c504d03fa/2.filter.Rmd#L53-L73