movPAindex: Calculate PAC index for each PAC in each condition.

In BMILAB/movAPA: movAPA: Modeling and Visualization of Dynamics of Alternative PolyAdenylation

Calculate PAC index for each PAC in each condition.

Description

movPAindex calculates index of each PAC, while movAPAindex calculates index for APA genes. method=ratio/geo is only allowed for APA genes, so these indices are only calculated for PACs in APA genes.

Usage

movPAindex(PACds, method, shan.ratio = FALSE)

Arguments

PACds	a PACDataset object.
method	should be "shannon","ratio", "geo". "shannon": tissue specificity; "ratio": ratio for APA sites (single PA genes are removed first); "geo": PUI by geometry mean (=log2(pA/all_PAs_geo_mean)), as in Shulman 2019 et al (single PA genes are removed first).
shan.ratio	Pass to specificityByShannon.

Value

A matrix of PA index.

• shannon: return a dataframe of [H (overall TS), Q_min (min TS), Q_min_tissue, Q for each tissue], in which smaller H or Q means higher tissue-specificity. If PA=0 in one sample, then the respective Qval is NA.

• "geo/ratio": return a dataframe of the same row# and col# of the PACds@counts.

See Also

Other comparison functions: movAPAindexDiff(), movAPAindex(), movAPAswitch(), movDEGene(), movDEPAC(), movUTRtrend(), plotCummPAindex()

Examples

data(PACds)
PAindex=movPAindex(PACds, method='ratio')
PAindex=movPAindex(PACds, method='geo')
PAindex=movPAindex(PACds, method='shannon')

BMILAB/movAPA documentation built on Jan. 3, 2024, 11:09 p.m.