diffPAL2PAgene: diffPAL2PAgene

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

Description

Analysis of significant difference in tail length of genes with two PAs.

Usage

diffPAL2PAgene(PAdf, PALdf, gff, d)

Arguments

PAdf	A dataframe of PA infomation.
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.

Details

This function was used to analyze the data for genes with two PA sites showing significant differences in tail length between the two PA sites.The function will use four difference significance test methods to find all genes with significant difference in tail length in the provided data and make a UpSet graph.

Value

The function returns a dataframe of result. The result data frame 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.

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