User: genogeno

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genogeno0
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Posts by genogeno

<prev • 23 results • page 1 of 3 • next >
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Comment: C: Sorting the haplotypes by similarities of SNPs in R
... Thank you! Unfornutaly, it doesn't give what I want. I guess it is more complicated than that. ...
written 6 months ago by genogeno0
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Sorting the haplotypes by similarities of SNPs in R
... I have a data set and I want to sort it in the following way in R. I hope I can explain clearly. 1- Sort by the elements seen in the main column (focal SNP). This will give us two chunks, one chunk with all As and one chunk with all Gs. 2- Then for the first chunk, move to the -1 column pos ...
haplotype snp clustering written 7 months ago by genogeno0 • updated 5 months ago by Biostar ♦♦ 20
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Comment: C: Convert numeric alleles into letters
... I see ok thank you very much. I really appreciate. ...
written 10 months ago by genogeno0
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Comment: C: Convert numeric alleles into letters
... I see thank you very much for your interest. It works but it assigns 1,2,3,4 instead of A,T,G,C according to legend. Why? ...
written 10 months ago by genogeno0
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Comment: C: Convert numeric alleles into letters
... Sorted: 134788398 134792091 134793655 134794177 134796050 NA06984_B 0 0 0 0 0 NA07055_B 0 0 0 0 0 NA11917_B 0 0 0 0 0 NA10850_B 1 1 1 0 0 NA07022_B 0 0 0 0 0 NA11992_B 0 0 0 0 0 NA12282_A 0 0 0 0 0 NA12282_B 1 1 1 0 0 NA11917_A 1 0 1 1 0 Legend: rsID ...
written 10 months ago by genogeno0
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Comment: C: Convert numeric alleles into letters
... I am not sure how I can provide a reproducible code but I hope the structures of the variables help you. > str(sorted) 'data.frame': 34 obs. of 683 variables: $ 134788398: int 0 0 0 1 0 0 0 1 1 0 ... $ 134792091: int 0 0 0 1 0 0 0 1 0 0 ... $ 134793655: int 0 0 0 1 0 0 ...
written 10 months ago by genogeno0
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Comment: C: Convert numeric alleles into letters
... Hi Gennady, I am trying to run following code but it gives an error. result<- sorted[, lapply(.SD, function(x) { ifelse(x == 0, legend$a0, legend$a1) })] **Error in .subset(x, j) : invalid subscript type 'list'** How can I fix it? Thanks ...
written 10 months ago by genogeno0
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HapMap 3 phased haplotype
... Hi, I need to get HapMap 3 phased haplotype data. Where can I find it? Actually I need these data for specific populations and a specific gene. What is the easiest way to find data? I hope I can find an answer. Thank you! ...
snp written 15 months ago by genogeno0
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haplotypes from ped/vcf file
... Hi, I have vcf and ped file of CEU from 1000 Genomes. I need to obtain haplotype data with each column containing SNPs. How can I get these data set? Thank you! ...
snp written 15 months ago by genogeno0
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Answer: A: Problem with Haploview loading of files from latest (Sept 15-17 2014) update to
... Hi, I have same problem. Is there anybody who can help? Thanks! ...
written 15 months ago by genogeno0

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Popular Question 10 months ago, created a question with more than 1,000 views. For pca in eigenstrat

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