plot.SMSC: Plot the "SMSC" object

In KarimOualkacha/SmoothMSC: The smooth methylation status calling (SMSC) procedure

Description

An Illustrated Plot Summary (see: Article)

Usage

plot.SMSC(ratio, org, t, fit)

Arguments

ratio	the observed count of C reads at the ith CpG site divided by the observed count of C reads and T reads for each site i
org	The statue of the ith Cpg site, 0 : the site is unmethylated, 1 : the site is methylated
t	The location of the site i on a chromosome
fit	SMSC object

Examples

#### MSC scenario
data(Data_MSC)
#### HHM scenario
data(Data_HHM)

y <- Data_MSC #### or y <- Data_HHM

origin = y$origin
ratio=y$Ccount/y$CT
position = y$position

fit0<-SMSC(y$Ccount, y$CT,y$position, method="MSC")
plot(ratio,origin,position,fit0)

fit1<-SMSC(y$Ccount, y$CT,y$position, method="KNN1")
plot(ratio,origin,position,fit1)

fit2<-SMSC(y$Ccount, y$CT,y$position, method="KNN2")
plot(ratio,origin,position,fit2)

fit3<-SMSC(y$Ccount, y$CT,y$position, method="Locfit")
plot(ratio,origin,position,fit3)

KarimOualkacha/SmoothMSC documentation built on May 8, 2019, 4:49 p.m.