promoterDHcR: Calculate promoter DHcR

In HengPan2007/MethSig: DNA Methylation Drivers Inference

Description

Promoter differentially hypermethylated cytosine ratio (DHcR) is defined as the ratio of hypermethylated cytosines (HCs) to the total number of promoter CpGs profiled.

Usage

promoterDHcR(file_name, pro, min_cpgs = 5)

Arguments

file_name	A tab-separated values input file (without a header line) containing details of differentially methylated cytosines (DMCs) with following columns (V1 to V11): chr, pos, numC in control, numC + numT in control, numC in tumor, numC + numT in tumor, CpG methylation ratio (tumor methylation / control methylation), chi-squared test p-value, adjusted p-value, significance, hyper or hypo in tumor. Details of generating this type of files were described in Pan et al., Cancer Systems Biology, 2018.
pro	A GRanges object containing promoter annotation.
min_cpgs	An integer value defining the minimum number of covered CpGs for each promoter.

Value

A data frame summarizing promoter DHcR levels.

• Hugo: Hugo symbol

• Depth: Average sequencing depth

• HCs: Number of HCs

• CpGs: Number of covered CpGs

• DHcR: DHcR level

Examples

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

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