geneAnno: Tail quantitative by alignment

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

Description

geneAnnoAdd genetic information to the tail after alignment.

Usage

geneAnno(tailDF, refPath, bamdf, GFF, longRead)

Arguments

tailDF	The tailScan dataframe.This parameter is required if the sequence type is shortreads, and omitted if the sequence type is longreads.
refPath	The path of Reference conversion table.
bamdf	The output dataframe of the function tailMap. Include at least read_num,chr,strand,coord.
GFF	GFF file, can be GFF/GTF/GFF3, or TXDB comment package.It is recommended to use the TXDB annotation package, but be careful about the correspondence of the reference genome version.
longRead	Boolean value.If your sequence type is longreads this parameter is T, otherwise it is F, and the default is T.

Details

This function annotates the gene information, including the gene ID and gene type, using the tail of the matched gene from the GFF file.

Value

Added tail table of gene annotation information.Include at least read_num,tail,PAL,chr,strand,gene,gene_type,tailType,read_type and sample.

See Also

[tailMap()] to quantitative tails without sequence algin.

Other Poly(A) Tail length quantification functions: faBuilder(), tailMap(), tailScan()

Examples

library(movAPA)
library(TxDb.Mmusculus.UCSC.mm10.knownGene)
data(GV1tailDF)
data(GV1tailMapre)
AnnotedTails =
geneAnno(tailDF=GV1tailDF,bamdf=GV1tailMapre,GFF=TxDb.Mmusculus.UCSC.mm10.knownGene,longRead=F)

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