raw_ALSvcf: GWAS Amyotrophic lateral sclerosis ieu open GWAS project -...
In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS
raw_ALSvcf R Documentation
GWAS Amyotrophic lateral sclerosis ieu open GWAS project - Subset
Description
VCF (VCFv4.2) of the GWAS Amyotrophic lateral sclerosis ieu
open GWAS project Dataset: ebi-a-GCST005647.
A subset of 99 SNPs
Format
vcf document with 528 items relating to 99 SNPs
Details
A VCF file (VCFv4.2) of the GWAS Amyotrophic lateral sclerosis ieu
open GWAS project has been subsetted here to act as an example summary
statistic file in VCF format which has some issues in the formatting.
MungeSumstats can correct these issues and produced a standardised summary
statistics format.
ALSvcf.vcf
NA
Source
The summary statistics VCF (VCFv4.2) file was downloaded from
https://gwas.mrcieu.ac.uk/datasets/ebi-a-GCST005647/
and formatted to a .rda with the following:
#Get example VCF dataset, use GWAS Amyotrophic lateral sclerosis
ALS_GWAS_VCF <- readLines("ebi-a-GCST005647.vcf.gz")
#Subset to just the first 99 SNPs
ALSvcf <- ALS_GWAS_VCF[1:528]
writeLines(ALSvcf,"inst/extdata/ALSvcf.vcf")
neurogenomics/MungeSumstats documentation built on Aug. 10, 2024, 5:59 a.m.
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| raw_ALSvcf | R Documentation |
GWAS Amyotrophic lateral sclerosis ieu open GWAS project - Subset
Description
VCF (VCFv4.2) of the GWAS Amyotrophic lateral sclerosis ieu open GWAS project Dataset: ebi-a-GCST005647. A subset of 99 SNPs
Format
vcf document with 528 items relating to 99 SNPs
Details
A VCF file (VCFv4.2) of the GWAS Amyotrophic lateral sclerosis ieu open GWAS project has been subsetted here to act as an example summary statistic file in VCF format which has some issues in the formatting. MungeSumstats can correct these issues and produced a standardised summary statistics format.
ALSvcf.vcf
NA
Source
The summary statistics VCF (VCFv4.2) file was downloaded from
https://gwas.mrcieu.ac.uk/datasets/ebi-a-GCST005647/
and formatted to a .rda with the following:
#Get example VCF dataset, use GWAS Amyotrophic lateral sclerosis
ALS_GWAS_VCF <- readLines("ebi-a-GCST005647.vcf.gz")
#Subset to just the first 99 SNPs
ALSvcf <- ALS_GWAS_VCF[1:528]
writeLines(ALSvcf,"inst/extdata/ALSvcf.vcf")
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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