readSnpsPed: Conversion to single column per locus from plink file via LEA...
In nfj1380/mrIML: Multi-Response (Multivariate) Interpretable Machine Learning
readSnpsPed R Documentation
Conversion to single column per locus from plink file via LEA functionality
Description
Conversion to single column per locus from plink file via LEA functionality
Usage
readSnpsPed(pedfile, mapfile)
Arguments
pedfile
A file location.
mapfile
A file location.
Details
Function to import SNP data from a plink format into a format
suitable for MrIML predicts (presence/absence of an alelle for each locus).
Currently if there is missing data (NAs) it either imputes them as the mode
or leaves them. A histogram is also produced of the missing data.
Value
A tibble.
Examples
snps <- readSnpsPed("FILE_NAME.plink.ped", "FILE_NAME.plink.map.map")
X <- filterRareCommon(snps, lower = 0.4, higher = 0.7)
nfj1380/mrIML documentation built on June 2, 2025, 1:03 a.m.
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| readSnpsPed | R Documentation |
Conversion to single column per locus from plink file via LEA functionality
Description
Conversion to single column per locus from plink file via LEA functionality
Usage
readSnpsPed(pedfile, mapfile)
Arguments
pedfile |
A file location. |
mapfile |
A file location. |
Details
Function to import SNP data from a plink format into a format suitable for MrIML predicts (presence/absence of an alelle for each locus). Currently if there is missing data (NAs) it either imputes them as the mode or leaves them. A histogram is also produced of the missing data.
Value
A tibble.
Examples
snps <- readSnpsPed("FILE_NAME.plink.ped", "FILE_NAME.plink.map.map")
X <- filterRareCommon(snps, lower = 0.4, higher = 0.7)
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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