Description Usage Arguments Value Examples
Promoter differentially hypermethylated cytosine ratio (DHcR) is defined as the ratio of hypermethylated cytosines (HCs) to the total number of promoter CpGs profiled.
1 | promoterDHcR(file_name, pro, min_cpgs = 5)
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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. |
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
1 2 | promoterDHcR(file_name = system.file("extdata", "DMC.SRR2069925.txt", package = "MethSig"),
pro = makeHG19Promoters())
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