Sort all genes in the dataset by their Kullback Leibler distance ratios or p-values.
timeSeq.sort(genenames,npde,pde,table,count,pvalue)a vector of gene names.
a vector of Kullback Leibler distance ratios or p-values for NPDE genes.
a vector of Kullback Leibler distance ratios or p-values for PDE genes.
gene expression values.
the number of exons or replicates for each gene.
logical:indicating if p-values are returned.
A list with components
dataframe of NPDE genes sorted by KLRs or p-values.
dataframe of PDE genes sorted by KLRs or p-values.
gene expression values for each gene, corresponding to npde.list.
gene expression values for each gene, corresponding to pde.list.
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.
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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