RNA-Seq Generation/Modification for Simulation


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Documentation for package ‘seqgendiff’ version 1.2.4

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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.