User: akang
akang • 90
- Reputation:
- 90
- Status:
- Trusted
- Location:
- Last seen:
- 1 month ago
- Joined:
- 3 years, 10 months ago
- Email:
- a******@gmail.com
Posts by akang
<prev
• 65 results •
page 1 of 7 •
next >
0
votes
2
answers
134
views
2
answers
Comment:
C: R, plot text table
... Since it is a biological dataset I think Biostars community suits it the best. This particular problem aims at visualizing a viral gene segment from different samples and understand its origin.
There are all sort of biological datasets and this might be a new one for the community. Here is an examp ...
written 4 weeks ago by
akang • 90
0
votes
2
answers
134
views
2
answers
Comment:
C: R, plot text table
... Added some information about the example data. ...
written 4 weeks ago by
akang • 90
0
votes
0
answers
274
views
0
answers
... 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)$pop) # pai ...
written 7 months ago by
akang • 90
0
votes
0
answers
358
views
0
answers
... I have calculated the pairwise distances between populations using adegenet (R package) and have plotted them using a boxplot. Labels on the Y axis are overlapping so i want to change the font size. How do I do that? Here is my code
temp <- pairDistPlot(mydata, grp=mydata$pop)
temp$boxpl ...
written 7 months ago by
akang • 90
0
votes
0
answers
286
views
0
answers
... 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 8 months ago by
akang • 90
0
votes
0
answers
338
views
0
answers
... 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 9 months ago by
akang • 90
0
votes
1
answer
1.5k
views
1
answers
... You can use kinship matrix or GRM which accounts for population structure. For LDAK see –calc-kins-direct and for GCTA see --grm. ...
written 23 months ago by
akang • 90
0
votes
2
answers
2.4k
views
2
answers
... 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 2.1 years ago by
akang • 90
0
votes
5
answers
975
views
5
answers
... Thanks everyone! With all your help I got it done! ...
written 2.1 years ago by
akang • 90
0
votes
5
answers
975
views
5
answers
... 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 2.1 years ago by
akang • 90
Latest awards to akang
Popular Question
7 months ago,
created a question with more than 1,000 views.
For Deleting the Individuals from genlight/genind object in adegenet
Popular Question
7 months ago,
created a question with more than 1,000 views.
For Phylogenetic tree in Adegenet
Popular Question
9 months ago,
created a question with more than 1,000 views.
For Phylogenetic tree in Adegenet
Popular Question
9 months ago,
created a question with more than 1,000 views.
For How to increase the resolution of the figures for publication
Popular Question
23 months ago,
created a question with more than 1,000 views.
For How to increase the resolution of the figures for publication
Popular Question
23 months ago,
created a question with more than 1,000 views.
For How to merge two illumina 50k Bovine beadchip data sets. The two datasets have SNP id in different formats.
Popular Question
23 months ago,
created a question with more than 1,000 views.
For CNV calling and analysis from Affymetrix Axiom 50K SNP chip
Popular Question
23 months ago,
created a question with more than 1,000 views.
For How to plot LD decay?
Popular Question
23 months ago,
created a question with more than 1,000 views.
For Request for BEAGLE tutorial
Popular Question
23 months ago,
created a question with more than 1,000 views.
For Converting 0 1 2 in a format recognized by plink
Popular Question
23 months ago,
created a question with more than 1,000 views.
For Genotype count in a VCF file
Popular Question
23 months ago,
created a question with more than 1,000 views.
For How to determine the haplotypes using Beagle
Popular Question
23 months ago,
created a question with more than 1,000 views.
For How to check and extract if a SNP is heterozygous or homozygous in a vcf file from the SNP ID
Popular Question
23 months ago,
created a question with more than 1,000 views.
For Population-wise decay of linkage disequilibrium (LD)
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1531 users visited in the last hour