##############################################################################################################
#  README for WeightFunctions.R
# These function is an R-compliant function. 
# R is a free-downloadable software from http://www.r-project.org/
# 
#  Author: Yen-Yi Ho
#  Email: yho@umn.edu
#  Last Modified: April 17, 2013
#  Version: 1.0.1 
# License information: GNU GENERAL PUBLIC LICENSE version 3 @ http://www.gnu.org/licenses/gpl.html
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################ mylm function ###########################################################################
Description:It is an internal function. mylm function is for fast calculation of regression coefficient from linear regression model with intercept.  
Usage: mylm(x=x, y=y)
Arguments: 
X: covariate matrix (n x p), p is the number of covariates 
Y: (n x 1) matrix, for response variable

################ isna ###########################################################################
Description:It is an internal function. 

################ WTestt3 function usage############################################################################
Description: WTestt3 is a function for calculating weights using (SNP + E + D) data. 
Usage: WTestt3(data, ptrim1=sqrt(0.05), ptrim2=sqrt(0.05), floor=1)

Arguments: 
data: a matrix with obervations in rows and (SNP + E +D) in columns. SNP needs to have column names with character string "rs", and E needs to have column names with character string "ILMN" or "X". Disease (phenotype outcome) vector needs to be label as "D".   
ptrim1: The value to set Wle=floor, if Wle < chisq(1,ptrim1), default is sqrt(0.05)
ptrim1: The value to set Wed=floor, if Wed < chisq(1,ptrim2), default is sqrt(0.05)
floor: The value of Wld and Wed if Wle< chisq(1, ptrim1) or Wed < chisq(1, ptrim2)

Value: 
	WTestt3 returns p x 2 matrix, where p is the number of SNP markers. The first column is GWAS p value, and second column reports weight. 


Examples: 

######################
Example 1: 
source("WeightFunctions.R")
PubL<-read.delim("PubL.txt", header=TRUE, sep="\t")
PubE<-read.delim2("PubE.txt", header=TRUE, sep="\t")
PubD<-read.delim("PubD.txt", header=TRUE, sep="\t")
whL<-grep("rs", colnames(PubL))[1:10]
myL<-PubL[,whL]
whE<-grep("X", colnames(PubE))[1:10]
myE<-PubE[,whE]
D<-PubD[,7]
data<-cbind(myL, myE, D)
WTestt3(data)