PALdsa: PALdsa

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

Description

Analysis of significant difference of tail length under different conditions.

Usage

PALdsa(PAdf, PALdf, gff, d, mode, withViolinPlot, withUpsetPlot, SAoDMethod)

Arguments

PAdf	A dataframe of PA infomation without merge.
PALdf	A dataframe that contains the length information of all reads tails.
gff	Genome annotation stored in a GFF/GTF file or a TXDB R object can be used for annotating PACs. Please refer to movAPA for details.
d	distance to group nearby PACds, default is 24 nt.
mode	The PAL comparison mode, "PD" refers to comparing the tail length difference between the proximal and distal PA sites of each gene with two PACs."2PA" represents a direct comparison of tail length differences between the two PA loci of genes with two PACs, default for "PD".
withViolinPlot	Logical value variable, Whether to draw a violin diagram, see function DSA_ViolinPlot() for details, default is true.
withUpsetPlot	Logical value variable, Whether to draw a upset diagram, see function DSA_UpsetPlot() for details, default is true.
SAoDMethod	one of "KS", "MWU", "ME", "Wilcox" and "ALL".

Details

The poly(A) tail length of genes with two PACs was analyzed for significant difference.It is feasible to directly analyze whether there is a significant difference in tail length between the two PACs, or to annotate PACs as the proximal PA site and the distal PA site before conducting the significance analysis of tail length difference.

Value

By default, this function returns a list of two graphs and a dataframe, or only a dataframe if no drawing operation has been performed. The result dataframe contains 7 column contents, the first column is geneID, and the second and third columns are the median tail lengths under different conditions. The remaining four columns are p-values calculated by different difference significance test methods, each column corresponds to a difference significance test method, in which "lose" or "NAN" means that for some reason (probably too little data) this method has not been able to calculate the exact p-values.

See Also

[DSA_ViolinPlot()] to draw a violin diagram of the result of differential tail length analysis.

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

Examples

library(movAPA)
library(TxDb.Mmusculus.UCSC.mm10.knownGene)
gff <- parseGenomeAnnotation(TxDb.Mmusculus.UCSC.mm10.knownGene)
data(AnnotedTails)
files = system.file("extdata", "./output/PAs/PAs.txt", package = "PolyAtailor", mustWork = TRUE)
PAs <- read.table(files,header=TRUE,sep=" ")
diffPAL2PAgenes <-
PALdsa(PAs,AnnotedTails,gff,mode="PD",SAoDMethod="ME",withViolinPlot=TRUE,withUpsetPlot=F)

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