User: amitgourav.ghosh12

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Posts by amitgourav.ghosh12

<prev • 26 results • page 1 of 3 • next >
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Comment: C: VCFtools: --window-pi and --from-bp --to-bp produces different start and ending
... Hello Sir, I am facing the same problem. I somewhat managed to get one whole region to come as one in Tajima's D calculation but I am unable to do so for the pi calculation. Did you find a way to overcome this problem? I yes, can you please suggest me what to do? Thanking you, Amit ...
written 6 months ago by amitgourav.ghosh1230
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Comment: C: Tajima's D Using SNP data ONLY
... Even I also have SNP data, can you please suggest how to compute Tajima's D without vcf files? Thank you! ...
written 7 months ago by amitgourav.ghosh1230
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Comment: C: How to do Tajima's D analysis?
... Hello Sir, indeed there are plenty of questions in the site. What I learnt till now is that one can use the package "pegas" in R or use dnasp v.5 or vcf tools for this purpose. I have binary format files from plink and the individuals respective MAFs, but not sequences. I am planning to download vcf ...
written 7 months ago by amitgourav.ghosh1230
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How to do Tajima's D analysis?
... Can anyone please suggest how to do Tajima's D analysis and the software required? Or can you please provide me with the links of similar answers. I want to detect signature of positive selection of certain alleles in my database. ...
genome snp written 7 months ago by amitgourav.ghosh1230
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Comment: C: How to do pca plot from .eigenval and .eigenvec files from Plink in R.
... Yes I plan to do so, I tried plotting it in R using ggplot, the colour reference took up the whole area instead of the plot. I managed to plot it in Excel with the colours, but I presume it is mostly for visualisation only. The name of the add-in is XLMiner Data Visualisation. If I point the cursor ...
written 9 months ago by amitgourav.ghosh1230
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Comment: C: How to do pca plot from .eigenval and .eigenvec files from Plink in R.
... I just finished counting the unique population groups in the samples. There were 254 different ethnicities in the sample size of 1977. ...
written 9 months ago by amitgourav.ghosh1230
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Comment: C: How to do pca plot from .eigenval and .eigenvec files from Plink in R.
... Great! I feel this is exactly what I wanted. Thank you Sir! Regarding Abkhazia, yes you are almost correct. This region is bit norther up in Georgia. Situated in the eastern coast of Black Sea. Last but not the least, it is a disputed territory of Georgia which enjoyed some autonomy while it was pa ...
written 9 months ago by amitgourav.ghosh1230
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Comment: C: How to do pca plot from .eigenval and .eigenvec files from Plink in R.
... Wow! Your advice might give me good head start about the ways to proceed or just to toy around the data to learn things in a playful manner. Please accept my gratitude for your kind guidance. My file looks like the one down below (actually has 1977 individuals after filtering), I can plot the eigen ...
written 9 months ago by amitgourav.ghosh1230
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Comment: C: How to do pca plot from .eigenval and .eigenvec files from Plink in R.
... Thank you very much for your kind advice! It was successful, now I am trying add colours to the plot according to their groups(ethnicities) and finding them to be a bit daunting. Thank you very much again! ...
written 9 months ago by amitgourav.ghosh1230
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Comment: C: How to do pca plot from .eigenval and .eigenvec files from Plink in R.
... Thank you Sir! I did use that file, now I am trying to add colours according to groups(ethnicities) in the graph. ...
written 9 months ago by amitgourav.ghosh1230

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