Zhengdeng Lei, PhD

Zhengdeng Lei, PhD

2009 - Present Research Fellow at Duke-NUS, Singapore
2007 - 2009 High Throughput Computational Analyst, Memorial Sloan-Kettering Cancer Center, New York
2003 - 2007 PhD, Bioinformatics, University of Illinois at Chicago

Friday, March 22, 2013

linear regression for multiple times


setwd("E:\\Projects\\8.ComBAT\\ComBat201\\NormalMarker")
data <- read.table("ComBat201T_orderbyDIM.txt", header = T, sep = "\t", row.names=1)

attach(data)

vars <- colnames(data)

res.out <- vector()
res.out[1] <-  paste("model", "r.squared", "coef.Subtype.Mes", "T.Stage", "Subtype.Meta", "Subtype.Mes:T.Stage", "T.Stage:Subtype.Meta" , "pval.Subtype.Mes", "T.Stage", "Subtype.Meta", "Subtype.Mes:T.Stage", "T.Stage:Subtype.Meta", sep=", ")
for (i in 6:26)
{
command <- paste("lm(", vars[i], " ~ Subtype.Mes*T.Stage+Subtype.Meta*T.Stage)", sep="")
lm.res <- eval(parse(text = command))
summary(lm.res)$r.squared
summary(lm.res)$coefficients[2] #regression.coef
summary(lm.res)$coefficients[3] #regression.coef

summary(lm.res)$coefficients[8] #pval

coef <- summary(lm.res)$coefficients

res.out[i-4] <- paste(command, summary(lm.res)$r.squared, coef[2],coef[3], coef[4], coef[5], coef[6], coef[20],coef[21], coef[22], coef[23],coef[24],sep=", ")
}

write.table(res.out, file="linear.model.TStage_subtype.txt", sep = "\t", quote=F, row.names=F, col.name=F)

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