plotPASignals: plotPASignals

In XHWUlab/PolyAtailor: a toolkit for analyzing poly(A) tail length dynamics from xxx RNA-seq data

Description

Draw the frequency distribution diagram of PA signal.

Usage

plotPASignals(PAdf, resultpath, bsgenome, signals, colorOfBar)

Arguments

PAdf	A dataframe that contains the PA information of all reads, Contains at least three columns: PAID, gene, ftr.
resultpath	The specified path to save barplot.
bsgenome	Reference genomes of the species of interest.
signals	The set of PA signal sequences of interest, such as signals=c("AATAAA","ATTAAA","AAGAAA","AATATA").
colorOfBar	The color of barplot, as input in hexadecimal form, defaults to "#196BE1".

Details

plot the probability distribution of the occurrence of user-specified or default PA signal within the first 50bp base range of PA site.

Value

A barplot.

See Also

[plotGenePAnumbers()] to plot the gene frequency distribution with different number of PA sites.

Other Visualization functions: DSA_UpsetPlot(), DSA_ViolinPlot(), PALdsa(), nonAanalysis(), plotGenePAnumbers(), plotPADistribution(), plotPALDistribution(), tailViso()

Examples

library("BSgenome.Mmusculus.UCSC.mm10")
bsgenome = BSgenome.Mmusculus.UCSC.mm10
data(PAs)
p <- plotPASignals(PAs,"./",bsgenome = bsgenome)

XHWUlab/PolyAtailor documentation built on Dec. 28, 2021, 12:13 a.m.