promoterPDR: Calculate promoter PDR

In HengPan2007/MethSig: DNA Methylation Drivers Inference

Description

Promoter proportion of discordant reads (PDR) is defined as the average PDR of all the CpGs inside.

Usage

promoterPDR(file_name, pro, min_cpgs = 3)

Arguments

file_name	A tab-separated values input file containing details of single CpG PDR with following columns: chr, start, strand, ConMethReadCount, ConUMethReadCount, DisReadCount, NAReadCount. Details of PDR were described in Landau et al., Cancer Cell, 2014. extdata/pdrCall_from_Bismark.py can be used to call PDR of an individual CpG from Bismark (Krueger et al., Bioinformatics, 2011) output files starting with CpG_OB or CpG_OT.
pro	A GRanges object containing promoter annotation.
min_cpgs	An integer value defining the minimum number of available CpGs for each promoter.

Value

A data frame summarizing promoter PDR levels.

• Hugo: Hugo symbol

• PDR: PDR level

Examples

promoterPDR(file_name = system.file("extdata", "PDR.SRR2069925.txt", package = "MethSig"),
            pro = makeHG19Promoters())

HengPan2007/MethSig documentation built on Aug. 1, 2020, 4:52 a.m.