Classify: Classification of SNPs based on theta estimates

Description Usage Arguments Details Author(s)

View source: R/Classify.R

Description

This function entails classification of SNPs based on the theta estimates (thetafile), genotype information (A regions file), and some internal files. Currently, this algorithm works for the Affymetrix 100K - Xba dataset.

Usage

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Classify(genotypefile = "",
         regionsfile = "",
	 thetafile = "",
	 callrate = 100)
	

Arguments

genotypefile

Name of the classified SNPs with the genotypes (required)

regionsfile

Character string specifying the directory AND name of regionsfile - e.g., "Xba.regions" (required)

thetafile

Character string specifying the directory AND name of thetafile (required)

callrate

Call Rate percentage; The user can specify any number from the list: 80,82,84,86,88,90,92,94,96,98,100. Default is 100%(optional)

Details

For each SNP, Mahalanobis distances from each chip's (theta A, theta B) ordered pair to the genotype centers is calculated. Each chip is assigned the genotype of the cluster which it is closest to (ie: AA, AB, BB).

Author(s)

Nusrat Rabbee <nrabbee@post.harvard.edu>, Gary Wong <wongg62@gmail.com>


RLMM documentation built on Nov. 8, 2020, 6:20 p.m.