timeSeq.screeplot: Scree Plot of Kullback Leibler Distance Ratios

Description Usage Arguments Author(s) References Examples

Description

Plot the scree plot for all genes in the dataset.

Usage

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

Arguments

timeSeq.obj

an object returned by timeSeq function

type

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

Author(s)

Fan Gao and Xiaoxiao Sun

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.

Examples

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data(simulate.dt)
attach(simulate.dt)
model.fit <- timeSeq(data.count, group.label, gene.names, reads, exon.level = FALSE,  n.cores = 1)
timeSeq.screeplot(model.fit, "lines")


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