User: HG

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HG30
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Posts by HG

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Comment: C: get calls in R
... Thank you very much for your reply and the correction for the data. Your code worked perfectly. ...
written 18 months ago by HG30
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Comment: C: get calls in R
... Here is part of the first dataframe: ID Sire.ID Dam.ID A D G B E H C F I part of the Second dataframe: ID Sire.ID Dam.ID marker1 marker2 marker3 marker4 marker5 marker6 marker7 marker8 marker9 D j K 12 21 11 11 12 22 11 22 11 ...
written 18 months ago by HG30 • updated 18 months ago by WouterDeCoster44k
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get calls in R
... Hi all, I have two dataframes: First data frame has three columns: ID, sire.ID, and Dam.ID The second dataframe has the same three columns plus genotyping calls for 17 markers in 17 columns. Here is what I need to be done in R: If sire.ID in the first dataframe exists in the ID column in the secon ...
R written 18 months ago by HG30
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Comment: C: Genotype frequency per sample
... Thanks for your comments. Yes, I need AA/Aa/aa. --het will return a text file with the following columns: 1. FamilyID, 2.Within-family ID, 3. Observed number of homozygotes, 4. Expected number of homozygotes, 5. Number of non-missing autosomal genotypes, 6. Method-of-moments F coefficient estimate. ...
written 23 months ago by HG30
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Comment: A: Genotype frequency per sample
... Hi, Plink files (my input files) are .map and .ped files: .ped file is as follows: A text file with the following fields: 1. Family ID 2. Individual ID 3. calls for each SNP .map file: A text file with no header file, and one line per variant with the following 3-4 fields: 1. Chromosome co ...
written 23 months ago by HG30 • updated 23 months ago by RamRS27k
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Genotype frequency per sample
... Hi everyone, I have a plink file and I want to get the distribution of calls (AA/Aa/aa) for each sample. How can I get to this? Any help would be appreciated. ...
snp written 23 months ago by HG30 • updated 23 months ago by chrchang5237.1k
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how to make bootstrapped tree using PLINK files?
... Hello all, I have PLINK files and I would like to make bootstrapped Nj tree for the populations? Could anyone suggest a method in R that can make this tree? Thanks ...
tree snp plink written 2.0 years ago by HG30 • updated 2.0 years ago by Kevin Blighe61k
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Comment: C: how to make bootstrapped tree in PVCLUST package with SNP genotyping data?
... The dataset is nearly uniform! I have 8 populations and in x I have [,1] to [,6] columns. Is it fine or I should have [,7] column, too? I got this error after the plot generated: .. Bootstrap (r = 1.38)... Done. Warning message: In a$p[] <- c(1, bp[r == 1]) : number of items to replace is not a ...
written 2.0 years ago by HG30
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Comment: C: how to make bootstrapped tree in PVCLUST package with SNP genotyping data?
... Worked perfectly.Great help! The only issue is that the location of each group in branches is different from what I got before in NJ tree (without Bootstraping value).Any idea? I got the plot but I found this warning message, too: Warning message: In a$p[] <- c(1, bp[r == 1]) : number of items ...
written 2.0 years ago by HG30
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Comment: C: how to make bootstrapped tree in PVCLUST package with SNP genotyping data?
... Thanks Kevin. It didnt work.Here is the error: x <- cmdscale(data.matrix(MyDist), k=iSampleNumber-1) Warning message: In cmdscale(data.matrix(MyDist), k = iSampleNumber - 1) : only 6 of the first 7 eigenvalues are > 0 ...
written 2.0 years ago by HG30

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