getTstats: Calculate moderated t statistic for each nucleotide

In leekgroup/derfinder: Differential expression analysis of RNA-seq data at base-pair resolution

Description

Modified (slimmed down) version of limma's eBayes, which uses a shrinkage approach to moderate t statistics from tests for differential expression across the genome.

Usage

getTstats(fit, trend = FALSE)

Arguments

fit	list with elements $sigma, $df.residual, $Amean (if trend=TRUE), $coefficients, and $stdev.unscaled. Usually the output of getLimmaInput (the $ebobject item), a more memory-efficient version of lmFit.
trend	as in eBayes, if TRUE, allow an intensity trend in the priors of variances (across genes/bps)

Value

A list with elements

tt	moderated t statistics for each gene/bp
logfchange	estimated log2 fold change on coverage between the groups, as estimated by a linear model

Author(s)

Alyssa Frazee

References

Smyth G (2004). "Linear models and empirical Bayes methods for assessing differential expression in microarray experiments." Statistical Applications in Genetics and Molecular Biology 3(1): Article 3.

See Also

getLimmaInput

leekgroup/derfinder documentation built on May 20, 2019, 11:30 p.m.