readSnpsPed: Conversion to single column per locus from plink file via LEA...
In nfj1380/mrIML: Multi Response 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 `dataframe` dataframe generated from mrvip function
`mapfile`	A `dataframe` response dataset

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.

Examples

## Not run: snps <- readSnpsPed("bobcat.plink.ped", "bobcat.plink.map.map") #NAs in data and interpolated as the mode. 
X <- filterRareCommon (snps, lower=0.4, higher=0.7) #these are harsh
## End(Not run)

nfj1380/mrIML documentation built on May 17, 2024, 7:41 a.m.