RNA-Seq Generation/Modification for Simulation

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Documentation for package ‘seqgendiff’ version 1.2.4

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

seqgendiff-package	seqgendiff: RNA-Seq Generation/Modification for Simulation
corassign	Group assignment that is correlated with latent factors.
effective_cor	Estimates the effective correlation.
est_sv	Estimate the surrogate variables.
fix_cor	Fixes an invalid target correlation.
permute_design	Permute the design matrix so that it is approximately correlated with the surrogate variables.
poisthin	Apply Poisson thinning to a matrix of count data.
select_counts	Subsample the rows and columns of a count matrix.
seqgendiff	seqgendiff: RNA-Seq Generation/Modification for Simulation
summary.ThinData	Provide summary output of a ThinData S3 object.
ThinDataToDESeqDataSet	Converts a ThinData S3 object into a DESeqDataSet S4 object.
ThinDataToSummarizedExperiment	Converts a ThinData S3 object into a SummarizedExperiment S4 object.
thin_2group	Binomial thinning in the two-group model.
thin_all	Binomial thinning for altering read-depth.
thin_base	Base binomial thinning function.
thin_diff	Binomial thinning for differential expression analysis.
thin_gene	Binomial thinning for altering total gene expression levels
thin_lib	Binomial thinning for altering library size.
uncorassign	Group assignment independent of anything.