normalizePACds: Normalize a PACdataset

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

Normalize a PACdataset

Description

normalizePACds returns a normalized PACds with @counts normalized.

Usage

normalizePACds(pacds, method = "TPM")

Arguments

pacds	a PACdataset.
method	normalization method, can be TPM/CPM/DEseq/DESeq2/EdgeR. CPM=TPM (after normalization, libsize of all columns are 1e6), DESeq=DESeq2.

Details

This function is used for normalization with different methods.

Value

A normalized PACdataset with pacds@counts normalized.

See Also

Other PACdataset functions: PACdataset-class, PACds, annotateByPAS(), annotatePAC(), createPACdataset(), get3UTRAPAds(), get3UTRAPApd(), length(), makeExamplePACds(), mergePACds(), plotPACdsStat(), rbind(), readPACds(), removePACdsIP(), scPACds, subscript_operator, summary(), writePACds()

Examples

data(PACds)
PACdsNorm=normalizePACds(PACds, method='TPM')

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