User: bha

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bha60
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Posts by bha

<prev • 41 results • page 1 of 5 • next >
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How to Ranking SNPs
... I have SNPs data sets in PLINK format. I wanted to choose top 1000 only (based on p-value or some other order). I wonder, can i do this in PLINK? Or any other programme can do this SNP ranking? Any suggestion please? ...
R plink snp written 6 weeks ago by bha60
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check relatedness of individuals
... I used 1000 g data sets to simulate the sequence. After performing simulation, I got 10K individuals, for some other analyses. I wonder, how i can check the relatedness of simulated individuals with original data (individuals)? Should I first calculate simple correlation of MAF from two data sets or ...
R next-gen genetics plink snp written 7 weeks ago by bha60 • updated 25 days ago by Biostar ♦♦ 20
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Comment: C: How to convert Haplotypes file to PLINK format data
... yes, i think it works well. ...
written 8 weeks ago by bha60
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Comment: C: How to convert Haplotypes file to PLINK format data
... Seems like that GTOOL can do this conversion: http://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#formats ...
written 8 weeks ago by bha60
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Comment: C: How to convert Haplotypes file to PLINK format data
... Yes, essentially they are. I have both genotypes, and haplotypes files. My main concern is to convert them to PLINK format, either haplotype or genotypes. Any idea please? ...
written 8 weeks ago by bha60
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Comment: C: How to convert Haplotypes file to PLINK format data
... these probabilities are 0s and 1s. And haplotypes are also in 0s and 1s. what do you suggest? ...
written 8 weeks ago by bha60
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Comment: C: How to convert Haplotypes file to PLINK format data
... Yes, i do have sample file as well. it's NOT zipped. here are the out files look like: http://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html#top ...
written 8 weeks ago by bha60
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Comment: C: How to convert Haplotypes file to PLINK format data
... The genotype file is exactly in the same format you mentioned in above link, and haplotype is 0s and 1s in standard file. The genytpe look like: SNP1 rs1 1000 A C 1 0 0 1 0 0 SNP2 rs2 2000 G T 1 0 0 0 1 0 SNP3 rs3 3000 C T 1 0 0 0 1 0 SNP4 rs4 4000 C T 0 1 0 0 1 0 SNP5 rs5 5000 ...
written 8 weeks ago by bha60
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Comment: C: How to convert Haplotypes file to PLINK format data
... yes! do you have any sense to convert this to PLINK format? ...
written 8 weeks ago by bha60
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How to convert Haplotypes file to PLINK format data
... I want to convert Haplotypes data to PLINK format (.map and .ped or binary .fam,.bim, .bed). I wonder, what is best software or R package, can do this easily? Has anybody came across this? Haplotype data is output file from HAPGEN2 (a programme which simulate the sequence data, but unfortunately, th ...
R plink bioinformatics written 8 weeks ago by bha60

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Popular Question 4 months ago, created a question with more than 1,000 views. For How do I remove duplicated by position SNPs using PLink?

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