User: bha

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bha0
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Posts by bha

<prev • 19 results • page 1 of 2 • next >
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Comment: C: How to convert plink.raw to map and ped files in any software
... I got two files 1) plink.raw (imputed genotypes as 012 format), and an other original map file say 2) plink.map file (which contain info for CHR, SNPIdentifier genetic distance and bpPOS). this is how i am doing; > famid <- FID patid <- IID fid <- PAT mid <- MAT s ...
written 5 days ago by bha0
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Comment: C: How to convert plink.raw to map and ped files in any software
... Yes, you are absolutely right. In original file, i have 3 heterozygous SNPs,but in current file (plink.raw 012) -this conflicting with original. I can't see 'G'. ...
written 5 days ago by bha0
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Comment: C: How to convert plink.raw to map and ped files in any software
... Do you meant to use this: > plink --ped plink.raw --map plink.map --out newData plink.raw is the file after converting 012 to 11, 22, and 11 (AA,CC,T)? ...
written 5 days ago by bha0
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Comment: C: How to convert plink.raw to map and ped files in any software
... I got this ped file using above R package (FID, IID, PAT,MAT,SEX,PHENO, and snps); 1 -6 4747 0 1 -9 1 1 2 2 1 1 1 -7 3211 0 2 -9 0 0 0 0 0 0 1 -8 4561 0 2 -9 1 1 2 1 1 1 1 -11 4745 0 1 -9 1 1 2 2 1 1 1 -12 4551 0 1 -9 0 0 0 0 0 0 1 -13 4538 0 1 -9 1 1 1 1 1 1 1 -14 10880 ...
written 5 days ago by bha0
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Comment: C: How to convert plink.raw to map and ped files in any software
... I tried with my data with (because my plink.raw is in 0,1,2): Type 1 : 1-column genotype matrix : minor allele count (0,1,2) and the output got accepted by PLINK. I have original genotype at each SNP (ATGC) - Just for learning; could you please write an example code, how to convert imputed da ...
written 5 days ago by bha0
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Comment: C: How to convert plink.raw to map and ped files in any software
... Thanks a lot for great help. I do have original data for mapping. your methods is also works, however, i tried something else which works more swiftly. As, PLINK wants two columns for each SNP, so I use this: > library(HapEstXXR) > Markers2 <- allele1to2(d_dimputed[, 7:61865]) which co ...
written 6 days ago by bha0 • updated 6 days ago by Kevin Blighe6.6k
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Comment: C: How to convert plink.raw to map and ped files in any software
... first 10 rows and columns plink.raw file: FID IID PAT MAT SEX PHENOTYPE snp1 snp2 snp3 snp4 1 6 4747 0 1 -9 1 1 1 1 1 7 3211 0 2 -9 0 1 0 0 1 8 4561 0 2 -9 0 0 0 0 1 11 4745 0 1 -9 0 2 0 2 1 12 4551 0 1 -9 2 2 0 NA 1 13 4538 0 1 -9 NA 0 1 0 1 14 10880 0 1 -9 2 0 2 0 ...
written 7 days ago by bha0
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Comment: C: How to convert plink.raw to map and ped files in any software
... I do have map file, I give a go with this > plink --ped MyImputedData.txt --map MyOriginalMap.map but ends up with error "token does not match". As I mentioned earlier, I got plink.raw (MyImputedData.txt ) from --recodeA (which convert alleles as 0, 1 and 2). So I think, plink expect 2 columns ...
written 7 days ago by bha0
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Comment: C: How to convert plink.raw to map and ped files in any software
... Kevin, many thanks for replying. Yes, I got plink.raw file from recode in plink. Actually I used (plink.raw after removing FID dad,mum,sex and pheno) file for imputing missing genotypes in an other programme called AlphaImpute. The output which got after imputation is in text file (which contain col ...
written 9 days ago by bha0
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How to convert plink.raw to map and ped files in any software
... I have a data files contains imputed genotypes with informations in the columns as: FamilyID IndividualID DAD MUM SEX Phenotype snp1 snp 2 .........snp60k this file is in plink.raw format, any idea how i can convert this in .map and ped plink format? ...
R plink snp sequencing written 9 days ago by bha0 • updated 9 days ago by Kevin Blighe6.6k

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