User: BlackHole

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BlackHole0
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Posts by BlackHole

<prev • 17 results • page 1 of 2 • next >
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How I make alignment data from vcf file
... Hello! I have 50 vcf file with many thousand snp, and number of this snd is different. I want to align Its to use its in gwas analysis How I make it using plink? ...
plink snp written 20 months ago by BlackHole0
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Using mQTL.NMR package in R
... Hi! Anybode use R packages mQTL.NMR for gwas analysis? I have problem with the obtained values of LOD. It approximatly equal for each phenotype (in my cases metabolits). And I think it is very strange ...
R gwas written 21 months ago by BlackHole0
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Comment: C: Converting Snp Genotype Data Into 0,1,2 Matrix Any Software?
... then a command to do transformation look like plink --ped ped.csv --map map.csv --recode12 ...
written 21 months ago by BlackHole0
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GWAS analysis on PLINK
... I want to do GWAS analyse using PLINK software. To understand it, I follow the tutorial, but in order to better understand I need an example datasets, i try to use link from tutorial (http://pngu.mgh.harvard.edu/~purcell/plink/res.shtml) , but it does not work Can I anywhere to find this data ? ...
plink snp written 21 months ago by BlackHole0 • updated 21 months ago by willgilks250
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(Closed) How find gene
... I have many snp (around 100 000) and I want to find all genes in which that snp are located.How can i do this ? And whether it is possible to do this using the R ? ...
snp written 22 months ago by BlackHole0
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Comment: C: How to convert txt file to ped and map using plink
... i have two files that look like : map.txt chr2 rs10185490 0 71166840 chr2 rs10185622 0 60289424 chr2 rs10185637 0 128422745 chr2 rs10185660 0 88463237 chr2 rs10185662 0 1964906 chr2 rs10185666 0 33696602 and ped.txt 0 Tri1 0 0 0 0 D D D D D D D D D D D D 0 Tri ...
written 23 months ago by BlackHole0
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How to convert txt file to ped and map using plink
... I am trying to convert a .txt and b.txt file to a1.ped and b1.map file using plink or R. I have read some manuals, but it seems that no one specifically mentions how to convert txt to ped and map. Can somebody help me out? P.S If there is another way (non-plink) of doing that, please do share it. ...
map plink ped txt written 23 months ago by BlackHole0
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Comment: C: Complement genotype
... i try to use for(i in nrow(Tri1_a)){ if(Tri1_a$V2[i] == 1){ if(Tri1_a$V1[i] == "T") Tri1_a$V3[i] = "A" if(Tri1_a$V1[i] == "A") Tri1_a$V3[i] = "T" if(Tri1_a$V1[i] == "G") Tri1_a$V3[i] = "C" if(Tri1_a$V1[ ...
written 23 months ago by BlackHole0 • updated 23 months ago by WouterDeCoster34k
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Complement genotype
... I am beginner in R, so apologize for such a simple question I have two columns V1 V2 T 1 C 0 A 1 if the column V2 is 1, then I want to replace nucleotide complementary if 0 is left as is I wrote a for functiom (in my many rows of data), but after his performance I get V1 ...
R written 23 months ago by BlackHole0 • updated 8 months ago by Biostar ♦♦ 20
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Which should contain the outfile in GenABEl
... I use convert.snp.ped from GenABEL packages to converts genotypic data to use its in logistic regression in R I have PED file that look like 0 Tri1 0 0 0 0 00 00 00 00 00 0 Tri2 0 0 0 0 AA 00 00 00 00 0 Tri3 0 0 0 0 AA AA AA AA AA 0 Tri4 0 0 0 0 AA AA AA AA AA 0 Tri5 0 0 0 0 AA ...
gene R snp written 24 months ago by BlackHole0 • updated 21 months ago by Biostar ♦♦ 20

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