User: Abdul Rafay Khan

gravatar for Abdul Rafay Khan
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Contact: alrafaykhan@gmail.com

Posts by Abdul Rafay Khan

<prev • 81 results • page 1 of 9 • next >
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Comment: C: LOD Score NaN Error
... but my data seems correct ...
written 5 days ago by Abdul Rafay Khan1000
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How to perform fst test using SNPs frequency?
... 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 ...
fst snp written 11 days ago by Abdul Rafay Khan1000
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LOD Score NaN Error
... 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 ...
lod score paramlink R written 13 days ago by Abdul Rafay Khan1000 • updated 13 days ago by zx87547.3k
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(Closed) How to perform fst test using SNPs frequency?
... 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. ...
frequency fst snp written 16 days ago by Abdul Rafay Khan1000
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Comment: C: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
... 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 19 days ago by Abdul Rafay Khan1000
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How to convert population SNPs frequency data into Plink format?
... 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 ...
plink snp written 19 days ago by Abdul Rafay Khan1000
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(Closed) Minor allele frequency and fst test
... 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 ...
maf fst written 20 days ago by Abdul Rafay Khan1000
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How do I calculate the haplotype frequencies in 1000 genome populations
... > 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? ...
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Principal components analysis of SNP data
... How many minimum snps are required to get reliable results from principal components analysis? ...
principal components pca snp written 23 days ago by Abdul Rafay Khan1000
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Comment: C: Calculate the allele frequency of specific sub-population using VEP
... Thank you, got the answer **Installation of Ensembl Rest API on R:** Install latest Rtools in base R from: https://cran.r-project.org/bin/windows/Rtools/ install.packages("githubinstall") library(githubinstall) library(devtools) devtools::install_github("timyates/EnsemblRest") ...
written 24 days ago by Abdul Rafay Khan1000

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