User: dam4l

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dam4l150
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Posts by dam4l

<prev • 23 results • page 1 of 3 • next >
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Extract genotype at single locus for all individuals in a PLINK binary ped file?
... I have genotype data (Illumina Global Screening Array) from ~700 individuals. I am also genotyping 1 SNP in using the TaqMan assay, and I need to check the concordance between the chip genotypes and the TaqMan genotypes for all individuals in my sample. To do this, I need to extract the genotype ...
plink snp written 5 months ago by dam4l150
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Converting SNP names from Illumina GSA array to rsID using PLINK
... Hi there, I am performing quality control on genotyping results from the Illumina Global Screening array. The SNP names throughout the PLINK format .map and .ped files are not in a consistent format (i.e., some are rsIDs, some have prefixes/suffixes, some are in chr:pos format, etc). Illumina provi ...
plink snp written 21 months ago by dam4l150
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Comment: C: Polygenic risk scoring using PRSice: Error in file(file, "rt") : cannot open the
... I have not a found a solution. ...
written 23 months ago by dam4l150
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Comment: C: Polygenic risk scoring using PRSice: Error in file(file, "rt") : cannot open the
... I have not found a solution. ...
written 23 months ago by dam4l150
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Polygenic risk scoring using PRSice: Error in file(file, "rt") : cannot open the connection
... I am trying to generate polygenic risk scores using the software PRSice. The base dataset has a quantitative phenotype. I want to generate the scores for subjects in a target dataset to test if PRS predicts drug response. I used the following code to generate the scores through PRSice: R --fi ...
prsice R snp written 2.2 years ago by dam4l150 • updated 23 months ago by bigfoot0
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Calculate genomic inflation factor lambda for meta-analysis run in PLINK?
... I meta-analyzed the results of 2 genome-wide association studies using PLINK. plink --meta-analysis file1 file2 + logscale qt --out results I created a Q-Q plot with the resulting p-values. The p-values look to be inflated. I am unsure whether this is resulting from inadequate control for pop ...
gwama gwas plink snp written 2.7 years ago by dam4l150
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Comment: C: Plot minor allele frequency distribution in R?
... I managed to do it using `freq = FALSE` with some additional information: h = hist(maf_file$MAF) h$density = h$counts/sum(h$counts) plot(h, freq = FALSE) ...
written 3.2 years ago by dam4l150
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Plot minor allele frequency distribution in R?
... Hi, I used PLINK (--freq) to get the minor allele frequencies for all SNPs in my GWAS. I would like to plot the distribution of MAFs in R with MAF on the x-axis and proportion of SNPs with a given MAF on the y-axis. I was able to plot the distribution of MAFs using the basic hist() function: h ...
maf gwas R written 3.2 years ago by dam4l150
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PLINK linear regression unwarranted error message?
... Hi, I am trying to run a GWAS with a quantitative phenotype in PLINK. I'm using linear regression with principal components from population structure analysis as covariates. The command is as follows: plink --bfile genotypefile --pheno pheno.txt --allow-no-sex --covar covariates --covar-name P ...
gwas plink regression written 3.2 years ago by dam4l150 • updated 3.2 years ago by chrchang5235.4k
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Comment: C: Normalize leptokurtic quantitative outcome measure in R?
... I plotted the values in the 'phen' column in a histogram to see the distribution - skewness was okay but it was leptokurtic. I'm using the values in 'phen' in a linear regression. The resulting p-vals from the regression are not normally distributed (I plotted them on -log(p) transformed QQ plot). A ...
written 3.3 years ago by dam4l150

Latest awards to dam4l

Great Question 18 months ago, created a question with more than 5,000 views. For Converting SNP from chr:pos to rs number using PLINK?
Popular Question 18 months ago, created a question with more than 1,000 views. For PLINK linear regression unwarranted error message?
Popular Question 18 months ago, created a question with more than 1,000 views. For Unknown error message in PLINK association analysis
Popular Question 18 months ago, created a question with more than 1,000 views. For Converting SNP names from Illumina GSA array to rsID using PLINK
Student 18 months ago, asked a question with at least 3 up-votes. For Converting SNP names from Illumina GSA array to rsID using PLINK
Student 21 months ago, asked a question with at least 3 up-votes. For Converting SNP from chr:pos to rs number using PLINK?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Converting SNP from chr:pos to rs number using PLINK?
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Converting SNP from chr:pos to rs number using PLINK?

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