example: This data set includes the calculation run on the Parkinson...

In saeidamiri1/mlgwsa: Genome Wide-Association Study (mlgwsa)

Usage

data("example")

Format

A dataset includes some calculation done on Parkinson data.

PDfeexample

result of running IBC on SNPdatafemPD

COfeexample

result of running IBC on SNPdatafemCO

dt1example

result of running Distwholeon informative variables

vsfeentRexample

result of HBF

dt2example

result of running Distwhole on HBF

Examples

data("example")
### Assume SNPdatafemCO and SNPdatafemPD are the SNPs of Parkinson- free and
### Parkinson disease females, respectively.
# data(SNPdatafemPD)
# data(SNPdatafemCO)
### We are not allowed to publish the data publically, so we created
### synthetic data SNPgroupC and SNPgroupD.

### Calculate the uncertainty of variables
#PDfeexample<-IBC(SNPdatafemPD)
#COfeexample<-IBC(SNPdatafemCO)

### Find the informative variables
vsfeent1example<-which(COfeexample>PDfeexample)
length(vsfeent1example)

### Calculate the distance between the data on the informative variables
#dt1example<-Distwhole(SNPdatafemPD,SNPdatafemCO,vsfeent1example)
### Calculate hierarchical dendrogram
hcdt1example<-hclust(as.dist(dt1example), method = "average", members = NULL)

### Define the label of data
##labfem<-c(rep("P",dim(SNPdatafemPD)[1]),rep("C",dim(SNPdatafemCO)[1]))
labfem<-c(rep("P",40),rep("C",101))

### plot the dendrogram
plot(hcdt1example,label=labfem)

Alpha<-0.80
hfbexample<-HFB(vsfeentRexample,Alpha)
length(hfbexample)

#### the folowing codes gives the dengrogram on the informative variables
#### obtained via HFB
#dt2example<-Distwhole(SNPdatafemPD,SNPdatafemCO,hfbexample)

### Calculate hierarchial dendrogram
hcdt2<-hclust(as.dist(dt2example), method = "average", members = NULL)
### plot the dendrogram
plot(hcdt2,label=labfem)

ts.plot(diff(hfbexample),xlab="diff", ylab="value")
hfbs3<-which(diff(hfbexample)<3)+1
ts.plot(diff(hfbexample[hfbs3]),xlab="diff", ylab="value")

saeidamiri1/mlgwsa documentation built on May 29, 2019, 9:10 a.m.