User: leeandroid

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leeandroid90
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Posts by leeandroid

<prev • 20 results • page 1 of 2 • next >
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Comment: C: Plot factors by specific column in ggplot
... I've tried factor both Assigned and Membership but it didn't work. I'm not sure I put it correctly: cap.dapc$Membership <- factor(cap.dapc$Membership, levels(factor(cap.dapc$Membership))) cap.dapc$Assigned <- factor(cap.dapc$Assigned, levels(factor(cap.dapc$Assigned))) I'm not sure ...
written 22 months ago by leeandroid90
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Comment: C: Plot factors by specific column in ggplot
... I've just added the color palette to my original post. You're right, I can only change the accession order. Another option would be changing the layout of the plot entirely, but I can't think of a clearer way to put it. ...
written 23 months ago by leeandroid90
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Plot factors by specific column in ggplot
... Hi everyone, I'm using [DAPC][1] to analyze the population structure of a GBS dataset. I was able to generate a table with the following: Population Accession Assigned Membership 1 C. a jal 1 9.051345e-63 2 ...
R order dapc written 23 months ago by leeandroid90
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Answer: A: Estimate relatedness in large dataset
... [VCFtools][1] is probably what you're looking for. However you should provide more information in order to get a better answer. [1]: https://vcftools.github.io/man_latest.html ...
written 2.0 years ago by leeandroid90
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Answer: A: PCA and statistics on SNPmatrix
... To pursue PCA you can use [SNPRelate][1] or [TASSEL][2] that has a user-frendly platform. [1]: http://corearray.sourceforge.net/tutorials/SNPRelate/ [2]: http://www.maizegenetics.net/tassel ...
written 2.2 years ago by leeandroid90
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Comment: C: DAPC different clustering results
... When running *find.clusters* the optimal number of clusters to retain is assessed based on BIC value and stored into *grp* same way as before. ...
written 2.3 years ago by leeandroid90
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Comment: C: DAPC different clustering results
... To run K = 2 to 20 you should use max.n.clust instead of n.clust, otherwise you are only runing k-means once. > n.clust an optinal integer indicating the number of clusters to be sought. If provided, the function will only run K-means once, for this number of clusters. If left as NULL, several ...
written 2.3 years ago by leeandroid90
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Comment: C: Retrieve list of kept SNP's after LD pruning
... Thank you for replying, Kevin. I was aware of the importance of chromosome nomenclature so I previously changed it to numeric values. Regarding variant ID's you're right. I was able to retrieve its original name by corresponding the row index in the snp_id_list to the row with the same index of the ...
written 2.3 years ago by leeandroid90
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Retrieve list of kept SNP's after LD pruning
... Hi everyone! I followed the [SNPRelate package tutorial][1] in order to filter a VCF by LD and finally pursued PCA. My problem is that by converting the VCF into GDS SNP's and Chromosomes ID's are also converted into a different nomenclature. >sample.id, a unique identifier for each sample. ...
vcf R gds snp snprelate written 2.3 years ago by leeandroid90 • updated 19 months ago by jessivannatta10
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Answer: A: From a vcf SNP file to a phylogenetic tree
... Try http://chibba.pgml.uga.edu/snphylo/ ...
written 2.4 years ago by leeandroid90

Latest awards to leeandroid

Epic Question 7 weeks ago, created a question with more than 10,000 views. For Change sample names in vcf
Popular Question 3 months ago, created a question with more than 1,000 views. For Filter VCF with txt
Popular Question 13 months ago, created a question with more than 1,000 views. For Filter VCF with txt
Great Question 16 months ago, created a question with more than 5,000 views. For Change sample names in vcf
Scholar 2.2 years ago, created an answer that has been accepted. For A: PCA and statistics on SNPmatrix
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Change sample names in vcf

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