diffPALdpPA: diffPALdpPA

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

Description

Analyzing whether there is a significant difference in polyA tail length between the proximal and distal PA sites of genes with two PACs.

Usage

diffPALdpPA(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 analyzes whether there is a significant difference in polyA tail length between the proximal and distal PA sites of genes with two PACs.

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.