taskBedsPlinkOut: Prepare shifted bed files for current task.
In kindlychung/CollapsABEL: An R package for quantitative CDH analysis
View source: R/taskBedsPlinkOut.R
Description
Read p values from the initial GWAS, get a list of SNPs by the given p value threshold,
extract the genotypes of these SNPs and create a new bed file, then generate shifted bed files
from this new bed file.
Usage
1
2
taskBedsPlinkOut(hub, taskName, plinkOutFile, pvalThresh = 0.05,
nMinShift = 1, nMaxShift)
Arguments
hub
Environment. QCDH data hub.
taskName
Character. Name of the task.
plinkOutFile
Character. PLINK assoc file of the initial GWAS.
pvalThresh
Numeric. p value threshold for extraction of SNPs.
kindlychung/CollapsABEL documentation built on May 20, 2019, 9:57 a.m.
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View source: R/taskBedsPlinkOut.R
Description
Read p values from the initial GWAS, get a list of SNPs by the given p value threshold, extract the genotypes of these SNPs and create a new bed file, then generate shifted bed files from this new bed file.
Usage
1 2 | taskBedsPlinkOut(hub, taskName, plinkOutFile, pvalThresh = 0.05,
nMinShift = 1, nMaxShift)
|
Arguments
hub |
Environment. QCDH data hub. |
taskName |
Character. Name of the task. |
plinkOutFile |
Character. PLINK assoc file of the initial GWAS. |
pvalThresh |
Numeric. p value threshold for extraction of SNPs. |
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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