getdeinfo: Get gene differential expression information from input...

In NWPU-903PR/Funm6AViewer: Visualization of single base differential m6A methylation sites and functional DmM genes

Description

Get gene differential expression information from input samples.

Usage

getdeinfo(grlist,
          txdb = TxDb.Hsapiens.UCSC.hg19.knownGene,
          savepath = NA)

Arguments

grlist	A list containing the reads count of IP/Input bam files under different condition and the id of each files. It can be generated using makegrreadsfrombam function.
txdb	The txdb famate genome annotation. You need to input it similar to "TxDb.Hsapiens.UCSC.hg19.knownGene" if use other genomes instead of hg19.
savepath	The file path where to save the result

Details

The DE analysis is done using DESeq2.

Value

By default, getdeinfo will output result of gene differential expresion information in both xls and data.frame which can used to calculate the DE score.

Author(s)

Songyao Zhang

References

Funm6AViewer: Visualization of single base differential m6A methylation sites and functional DmM genes.

NWPU-903PR/Funm6AViewer documentation built on April 25, 2021, 4:26 p.m.