More posts like this
-
No MAF filtering for GWAS
written by K Lee •Hello, I have question about MAF filtering in GWAS. As I know of, MAF-based variants filtering is a crucial step for GWAS since it filters …
-
Is it possible to detect of SNVs and InDels in low coverage WGS (5-10X) data?
written by wangziwei0010 •Hello, the Biostar community, What I know about low coverage WGS (or shallow WGS) data is that it is an economic technique for genomic copy …
-
Sample size calculation for GWAS (fixed number of controls)
written by khnHello I usually calculate sample sizes for GWAS using QUANTO. This time, the number of controls is already decided to 800, so QUANTO is not …
-
genomic inflation factor and how to use it to estimate adjusted P-values in GWAS?
written by AnaHi all, I have 3 questions regarding genomic inflation factor and how to use it to estimate adjusted p-value. I would appreciate any help. I …
-
Calculate genomic inflation factor lambda for meta-analysis run in PLINK?
written by dam4lI 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 …
-
Genomic Inflation Factor for GWAS of Quantitative Trait
written by brde4939 •Hello, I have performed a GWAS on a quantitative trait and would like to calculate the genomic inflation factor (lambda). Does anyone have advice on …
-
Determining best MCL inflation factor
written by Anand RaoI am trying to cluster orthologs (and paralogs) at the protein level. I seem to be getting groups that have very disparate proteins, because they …
-
At what point does does a departure from the normal constitute inflation (QQ plot)
written by Alexander Skates<p>I'm trying to interpret a QQ plot I have from Matrix eQTL, to see if there is a factor I haven't accounted for. I know …
-
Genomic Inflation Factor Lambda Too Low
written by mangeles.suarez •<p>I have a bed file with genotype data for around 450000 SNPs and 700 samples. I am performing a logistic regression analysis in PLINK with …
-
Large Genomic Inflation Factor In Gwas
written by Liyf •<p>I use eigenstrat to correct population structure in my multiple GWAS. I want to calculate the genomic inflation factor before correction, I think GIF should …
Anyone can shed some light on this?