coeplot: Estimated Coefficients Visualization

In GCAI.bias: Guided Correction Approach for Inherited bias (GCAI.bias)

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

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.

Value

a plot produced on the current graphic device

Note

index object should match the length of coe.lm

Author(s)

Guoshuai Cai

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)

GCAI.bias documentation built on May 1, 2019, 8:18 p.m.