GCAI.bias (version 1.0)

coeplot: Estimated Coefficients Visualization

Description

To plot estimated coefficients against their corresponding positions

Usage

coeplot(coe.lm, obj.index, ylim = c(-1, 1))

Arguments

coe.lm

a 1-column matrix of coefficients estimated from lm.estimate

obj.index

an object of index generated from index.mat.generation

ylim

the extremes of the range of y axis

Value

a plot produced on the current graphic device

Details

5 end of the mapped reads will be labeled 0 on x axis. Nucleotide A will be colored in red, T will be in yellowgreen, C will be in green and G will be in blue as the baseline.

References

Cai G, RNA-SEQUENCING APPLICATIONS: GENE EXPRESSION QUANTIFICATION AND METHYLATOR PHENOTYPE IDENTIFICATION, Ph.D. Thesis, 2013

See Also

lm.estimate,index.mat.generation

Examples

word<-81

data(obj.index)
data(train.dat.seq)
data(train.dat.counts)

train.index<-index.preprocess(train.dat.seq,word)
obj.train<-counts.preprocess(train.dat.counts)
obj.train[["index"]]<-train.index

coe.lm<-lm.estimate(obj.train,fit.cut.train=5)

coeplot(coe.lm,obj.index)