timeSeq (version 1.0.4)

timeSeq.screeplot: Scree Plot of Kullback Leibler Distance Ratios

Description

Plot the scree plot for all genes in the dataset.

Usage

timeSeq.screeplot(timeSeq.obj,type=c("barplot","lines"))

Arguments

timeSeq.obj

an object returned by timeSeq function.

type

type of plot: "barplot" for the bar plot and "lines" for the line graph.

References

Sun, Xiaoxiao, David Dalpiaz, Di Wu, Jun S. Liu, Wenxuan Zhong, and Ping Ma. "Statistical inference for time course RNA-Seq data using a negative binomial mixed-effect model." BMC Bioinformatics, 17(1):324, 2016.

Chong Gu. Model diagnostics for smoothing spline ANOVA models. Canadian Journal of Statistics, 32(4):347-358, 2004.

Chong Gu. Smoothing spline ANOVA models. Springer, second edition, 2013.

Chong Gu and Ping Ma. Optimal smoothing in nonparametric mixed-effect models. Annals of Statistics, pages 1357-1379, 2005a.

Wood (2001) mgcv:GAMs and Generalized Ridge Regression for R. R News 1(2):20-25

Examples

# NOT RUN {
data(simulate.dt)
attach(simulate.dt)
model.fit <- timeSeq(data.count,group.label,gene.names,exon.level=FALSE,pvalue=FALSE)
timeSeq.screeplot(model.fit,"lines")

# }