User: akang
akang • 90
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Posts by akang
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... I have used an R package called Adegenet to calculate pairwise Fst and pairwise genetic distances from an alignment file. But both the values are completely different.
matFst <- pairwise.fst(mydata,res.type="matrix") #pairwise Fst
temp <- pairDistPlot(mydata, other(mydata)$pop) # pai ...
written 3 months ago by
akang • 90
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... I have calculated the pairwise distances between populations using adegenet (R package) and have plotted them using a boxplot. Labels on the Y axis are overlapping so i want to change the font size. How do I do that? Here is my code
temp <- pairDistPlot(mydata, grp=mydata$pop)
temp$boxpl ...
written 3 months ago by
akang • 90
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... I have 5 groups in my study and I found that within and between mean group genetic distance is greater than 1 when calculated with MEGA X. Can someone help me understand what does that mean?
...
written 4 months ago by
akang • 90
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... Is there a program that can calculate effective population size (Ne) based on haploid sequence data? Most programs work with diploid SNP data as I know. ...
written 5 months ago by
akang • 90
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... You can use kinship matrix or GRM which accounts for population structure. For LDAK see –calc-kins-direct and for GCTA see --grm. ...
written 19 months ago by
akang • 90
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... I'm trying to do the same thing..just that my data is multi allelic. How do we calculate imputation accuracy for multi allelic data? Ill appreciate any help on that.Thanks! ...
written 21 months ago by
akang • 90
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... Thanks everyone! With all your help I got it done! ...
written 21 months ago by
akang • 90
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... Thanks for the code! But in real the file consists of over 20 columns and 2000 rows. So the code you wrote might not work. ...
written 21 months ago by
akang • 90
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... You are right! I changed that in the desired output section. ...
written 21 months ago by
akang • 90
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... Thanks! That sure does make it easy to understand. ...
written 21 months ago by
akang • 90
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