Find top confident effect sizes

edger_confects

Confident effect sizes based on the edgeR Quasi-Likelihood method, both linear and non-linear

limma_confects

Confident log2 fold changes using limma's treat function, linear effects only

limma_nonlinear_confects

Confident non-linear effect sizes using limma

nest_confects

General purpose function to find sets of discoveries for a range of effect sizes, controlling FDR

Diagnostic plots

confects_plot

Top confident effect sizes plot

rank_rank_plot

A plot to compare two rankings

confects_plot_me

Mean-expression vs effect size plot

Non-linear effect size definitions

These can be used with edger_confects or limma_nonlinear_confects.

effect_contrast_ratio

Ratio of contrasts effect.

effect_contrast

Simple linear contrast effect.

effect_gamma

Goodman and Kruskall's gamma, Yule's Q

effect_link_log2

Adapt an effect size object to work with coefficients estimated from log2 transformed data or with a log2 link function

effect_sd effect_rssm effect_rss

Standard-deviation of a set of coefficients as effect size

effect_shift effect_shift_stepdown effect_shift_stepup effect_shift_log2 effect_shift_stepdown_log2 effect_shift_stepup_log2

Shift of mass effect

Find top confident effect sizes for groups of features

For differential splicing, or shifts of transcript start or end.

edger_group_confects limma_group_confects

Group confects (differential exon usage, etc)

Group effect size definitions

These can be used with edger_group_confects or limma_group_confects.

group_effect_rssm

Group effect for differential splicing

group_effect_shift group_effect_shift_stepup group_effect_shift_stepdown group_effect_shift_log2 group_effect_shift_stepup_log2 group_effect_shift_stepdown_log2

Group effect for shifts in 5' or 3' end usage