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Questions tagged [gwas]

Genome-wide association study

Wikipedia

In genomics, a genome-wide association study (GWA study, or GWAS), also known as whole genome association study (WGA study, or WGAS), is an observational study of a genome-wide set of genetic variants in different individuals to see if any variant is associated with a trait. GWA studies typically focus on associations between single-nucleotide polymorphisms (SNPs) and traits like major human diseases, but can equally be applied to any other genetic variants and any other organisms.

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38 questions
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How to plot a Miami plot (GWAS) in R?

I'm looking for a function to run a Miami Plot (GWAS) which looks like this: I will have data for 2 different GWASes. To simulate the plot, you can use this dataset…
Gianmarco M
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Interactive Manhattan plot with string chromosome names

I'm trying to generate ManhattanPlot using Dash-plotly library for python: https://dash.plotly.com/dash-bio/manhattanplot I have SNP results data for plants like wheat which have chromosome names with letters e.g. 3A, 3B, 3D. Is is possible to…
MLearner
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Subsetting GWAS results by matching snp column from another file

I have a GWAS summary estimate file with the following columns (file 1): 1 chr1_1726_G_A 0.023 0.160 1 chr1_20184_GAATA_G 0.033 0.180 1 chr1_791101_T_TGG 0.099 0.170 file 2 chr1_20184_GAATA_G chr1_791101_T_TGG I would like to match…
AVA
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Error in count.fields(input.files[1]) : 'file' must be a character string or connection with gwasurvivr package

I am struggling with gwasurvivr package in R. The package contains all information and running perfectly given code and its own dataset inside the vignette. impute.file <- system.file(package="gwasurvivr", "extdata", …
Sandeep
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GWAS array to matrix

(this will be a supposition because the number are higher but to make things easier) Imagine that you have genotyped 10 persons and you have 3 SNIPS each one with 2 alels. then you end up with a matrix like this: , ,…
bubu kerokero
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y-axis breaks with ggplot2 for a manhattan plot

I have a manhattan plot of genetic information: It was generated using the qqman package https://cran.r-project.org/web/packages/qqman/vignettes/qqman.html) in R which takes a dataframe of P-values, chromosome position and a gene position (for any…
tacrolimus
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GenABEL on R4.2.2 Windows

I´m looking for a way to use GenABEL on R4.2.2 with Rstudio-2022.07.2-576. GenABEL is only accessible through the R archive with latest version from 2017 or github GenABEL-Project / GenABEL(https://github.com/GenABEL-Project/GenABEL). Was first…
AKP
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Unable to find the internal logging class: java.lang.NoClassDefFoundError: org/apache/spark/internal/Logging$class

I am trying to build spark cluster on DNAnexus platform. I tried creating spark context from jupyterlab notebook. import pyspark sc = pyspark.SparkContext() spark = pyspark.sql.SparkSession(sc) I get the following error stack trace. Py4JJavaError:…
Abhishek Shakya
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Examining position intersect and conditionally drop row based on P-values

I'm working my way through post-analysis of GWAS, where I have defined a list of independent SNPs associated with my trait. I'm trying to group my indep. SNPs in loci of +- 500KB. There are some independent SNP's which locus will overlap each other…
SorenRand
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Can analysis of GWAS/WES/WGS be performed with DNA from saliva in combination with DNA from blood?

Can statistical analyses (GWAS/WES/WGS) be performed with DNA from saliva in combination with DNA from blood? Is there a chance of bias? First, I think DNA=DNA, in other words, no matter how the 'DNA code' is collected. But there may be unexpected…
P.Roberto Bakker ev Doornebal
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Lifting over GWAS summary statististic file from build 38 to build 37

I am using the UCSC lift over tool and the associated chain to lift over the results of my GWAS summary statistic file (a tab separated file) from build 38 to build 37. The GWAS summary stat file looks like: 1 chr1_17626_G_A 17626 A G 0.016 -0.0332…
AVA
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Lassosum: exclusively for continuous traits?

I am trying to understand the method lassosum proposed by Mak et al. (2017). For what I understand, the method is created to build Polygenic Scores based on GWAS summary statistics. However, I thought that the outcome could be of different types:…
a12456
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GWAS Catalog API

disease_trait = input("Enter disease trait to search: ") url = "https://www.ebi.ac.uk/gwas/rest/api/studies" query_params = {"diseaseTrait": disease_trait, "size": 200} headers = {"Accept": "application/json"} response = requests.get(url,…
BScpj
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What can cause undefined columns error in GAPIT?

I'm starting working with GAPIT for GWAS. Here is an error that I get while trying to run. the simplest GLM with my data: "[1] "GD does not mach GM in Manhattan !!!" Error in [.data.frame(GD, , !is.na(GI.MP[, 3])) : undefined columns selected In…
M.Tis
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Dataframe Filtering Issues (GWAS Catalog)

I am currently trying to filter out the rows in my dataframe that include the value "Alzheimer's disease" in the column marked "DISEASE/TRAIT" and put it into a new dataframe. If you could help it would be immenseley appreciated. The two images show…
Tommy Reed
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