User: akang

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akang90
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Posts by akang

<prev • 63 results • page 1 of 7 • next >
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Should the values of pairwise genetic distances and Fst be somewhat similar?
... 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)$pop) # pai ...
R adegenet written 3 months ago by akang90
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Change the font size of the Y axis of a boxplot
... I have calculated the pairwise distances between populations using adegenet (R package) and have plotted them using a boxplot. Labels on the Y axis are overlapping so i want to change the font size. How do I do that? Here is my code temp <- pairDistPlot(mydata, grp=mydata$pop) temp$boxpl ...
boxplot R adegenet written 3 months ago by akang90
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Within and between mean group genetic distance greater than 1 with MEGA X
... 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? ...
genetic distance written 4 months ago by akang90
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Calculate effective population size (Ne)
... 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. ...
effective population size sequence data ne written 5 months ago by akang90
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Answer: A: Estimating heritability using GCTA or LDAK in an admixed population
... 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 akang90
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Comment: C: How to calculate Imputation Accuracy Estimates like concordance with BEAGLE?
... 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 akang90
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Comment: A: Restructuring table: rows to column and interleaving columns
... Thanks everyone! With all your help I got it done! ...
written 21 months ago by akang90
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Comment: C: Restructuring table: rows to column and interleaving columns
... 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 akang90
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Comment: C: Restructuring table: rows to column and interleaving columns
... You are right! I changed that in the desired output section. ...
written 21 months ago by akang90
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Comment: C: Restructuring table: rows to column and interleaving columns
... Thanks! That sure does make it easy to understand. ...
written 21 months ago by akang90

Latest awards to akang

Popular Question 5 months ago, created a question with more than 1,000 views. For Phylogenetic tree in Adegenet
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Popular Question 19 months ago, created a question with more than 1,000 views. For How to plot LD decay?
Popular Question 19 months ago, created a question with more than 1,000 views. For Request for BEAGLE tutorial
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Popular Question 19 months ago, created a question with more than 1,000 views. For Genotype count in a VCF file
Popular Question 19 months ago, created a question with more than 1,000 views. For How to determine the haplotypes using Beagle
Popular Question 19 months ago, created a question with more than 1,000 views. For Population-wise decay of linkage disequilibrium (LD)

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