User: Abdul Rafay Khan
Abdul Rafay Khan • 1.1k
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Contact: alrafaykhan@gmail.com
Posts by Abdul Rafay Khan
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2
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1
answer
244
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1
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... Is there any way to add a sample number/name column to VEP result file when the merge vcf file of multiple samples is annotated with VEP. ...
written 10 months ago by
Abdul Rafay Khan • 1.1k
• updated
10 months ago by
Emily_Ensembl ♦ 21k
1
vote
0
answers
317
views
0
answers
... I have VCF file with multiple samples. How to list down the SNP present in more than one sample with sample ids.
...
written 10 months ago by
Abdul Rafay Khan • 1.1k
0
votes
0
answers
278
views
0
answers
Comment:
C: LOD Score NaN Error
... but my data seems correct ...
written 14 months ago by
Abdul Rafay Khan • 1.1k
1
vote
1
answer
313
views
1
answer
... How to perform fst test using SNPs frequency?
My data format:
SNPs Pop1 Pop2 Pop3 Pop4 Pop4 Pop5 Pop6 Pop7
rs2740574 0.974 0.9448 0.7921 0.9625 0.9616 0.902 0.3556 0.9161
rs1751034 0.8906 0.7586 0.798 0.8457 0.8223 0.8081 0.7413 0.747
...
written 15 months ago by
Abdul Rafay Khan • 1.1k
2
votes
0
answers
278
views
0
answers
... library(paramlink)
y = read.table("markers.txt", header=TRUE)
x = linkdat(y, model=1)
lod(x)
Result:
LOD: NaN
**Data:**
FAMID ID FID MID SEX AFF M_A1 M_A2
1 1 0 0 1 1 2 3
1 2 0 0 2 1 1 2
1 3 1 2 2 2 2 2
1 4 1 2 1 2 2 3
1 5 1 2 2 1 1 2
1 ...
written 15 months ago by
Abdul Rafay Khan • 1.1k
• updated
15 months ago by
zx8754 ♦ 9.4k
0
votes
0
answers
217
views
0
answers
... How to perform fst test using SNPs frequency?
My data format:
SNPs Pop1 Pop2 Pop3 Pop4 Pop4 Pop5 Pop6 Pop7
rs2740574 0.974 0.9448 0.7921 0.9625 0.9616 0.902 0.3556 0.9161
rs1751034 0.8906 0.7586 0.798 0.8457 0.8223 0.8081 0.7413 0.747
rs1414334 0.875 0.8453 0.7872 0.8831 0. ...
written 15 months ago by
Abdul Rafay Khan • 1.1k
0
votes
0
answers
10k
views
0
answers
... Hey Kelvin,
How to plot sub-population ("ACB","ASW","ESN","GWD","LWK","MSL","YRI", "CLM","MXL","PEL","PUR", "CDX","CHB","CHS","JPT","KHV", "CEU","FIN","GBR","IBS","TSI", "BEB","GIH","ITU","PJL","STU") in pca plot instead of "African","Hispanic","East-Asian","Caucasian","South Asian"? ...
written 15 months ago by
Abdul Rafay Khan • 1.1k
0
votes
0
answers
218
views
0
answers
... How to convert population SNPs frequency data into Plink format?
My format:
> SNP Ashkenazi Finnish European Other African/African American Latino East Asian
> rs2234922 0.1448 0.1567 0.1995 0.1965 0.3388 0.1076 0.1253
> rs3812718 0.5035 0.5446 ...
written 15 months ago by
Abdul Rafay Khan • 1.1k
0
votes
0
answers
436
views
0
answers
... I have SNPs data in the form of minor allele frequency of different populations,
how to calculate the fst test using this data and can we load such data in plink 1.9?
My data format:
SNP Ashkenazi Jewish_G Finnish_G Non-Finnish European_G Other_G African/African American_G Latino_G East Asian ...
written 15 months ago by
Abdul Rafay Khan • 1.1k
0
votes
0
answers
363
views
0
answers
... > I have haplotypes (CYP2D6.1, CYP2D6.2, CYP2D6.3, CYP2D6.4, CYP2D6.5,
> CYP2D6.6)
How do I calculate the haplotype frequencies these haplotypes in 1000 genome populations? ...
written 15 months ago by
Abdul Rafay Khan • 1.1k
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