raw_eduAttainOkbay: GWAS Educational Attainment Okbay 2016 - Subset
In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS
raw_eduAttainOkbay R Documentation
GWAS Educational Attainment Okbay 2016 - Subset
Description
GWAS Summary Statistics on Educational Attainment by Okbay et
al 2016:
PMID: 27898078 PMCID: PMC5509058 DOI: 10.1038/ng1216-1587b.
A subset of 93 SNPs
Format
txt document with 94 items
Details
GWAS Summary Statistics on Educational Attainment by Okbay et
al 2016 has been subsetted here to act as an example summary statistic file
which has some issues in the formatting. MungeSumstats can correct these
issues.
eduAttainOkbay.txt
NA
Source
The summary statistics file was downloaded from
https://www.nature.com/articles/ng.3552
and formatted to a .rda with the following:
#Get example dataset, use Educational-Attainment_Okbay_2016
link<-"Educational-Attainment_Okbay_2016/EduYears_Discovery_5000.txt"
eduAttainOkbay<-readLines(link,n=100)
#There is an issue where values end with .0, this 0 is removed in func
#There are also SNPs not on ref genome or arebi/tri allelic
#So need to remove these in this dataset as its used for testing
tmp <- tempfile()
writeLines(eduAttainOkbay,con=tmp)
eduAttainOkbay <- data.table::fread(tmp) #DT read removes the .0's
#remove those not on ref genome and withbi/tri allelic
rmv <- c("rs192818565","rs79925071","rs1606974","rs1871109",
"rs73074378","rs7955289")
eduAttainOkbay <- eduAttainOkbay[!MarkerName
data.table::fwrite(eduAttainOkbay,file=tmp,sep="\t")
eduAttainOkbay <- readLines(tmp)
writeLines(eduAttainOkbay,"inst/extdata/eduAttainOkbay.txt")
neurogenomics/MungeSumstats documentation built on Aug. 10, 2024, 5:59 a.m.
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| raw_eduAttainOkbay | R Documentation |
GWAS Educational Attainment Okbay 2016 - Subset
Description
GWAS Summary Statistics on Educational Attainment by Okbay et al 2016: PMID: 27898078 PMCID: PMC5509058 DOI: 10.1038/ng1216-1587b. A subset of 93 SNPs
Format
txt document with 94 items
Details
GWAS Summary Statistics on Educational Attainment by Okbay et al 2016 has been subsetted here to act as an example summary statistic file which has some issues in the formatting. MungeSumstats can correct these issues.
eduAttainOkbay.txt
NA
Source
The summary statistics file was downloaded from
https://www.nature.com/articles/ng.3552
and formatted to a .rda with the following:
#Get example dataset, use Educational-Attainment_Okbay_2016
link<-"Educational-Attainment_Okbay_2016/EduYears_Discovery_5000.txt"
eduAttainOkbay<-readLines(link,n=100)
#There is an issue where values end with .0, this 0 is removed in func
#There are also SNPs not on ref genome or arebi/tri allelic
#So need to remove these in this dataset as its used for testing
tmp <- tempfile()
writeLines(eduAttainOkbay,con=tmp)
eduAttainOkbay <- data.table::fread(tmp) #DT read removes the .0's
#remove those not on ref genome and withbi/tri allelic
rmv <- c("rs192818565","rs79925071","rs1606974","rs1871109",
"rs73074378","rs7955289")
eduAttainOkbay <- eduAttainOkbay[!MarkerName
data.table::fwrite(eduAttainOkbay,file=tmp,sep="\t")
eduAttainOkbay <- readLines(tmp)
writeLines(eduAttainOkbay,"inst/extdata/eduAttainOkbay.txt")
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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