methylKit (version 0.9.5)

adjust.methylC: Adjust measured 5mC levels using 5hmC levels

Description

Measured 5mC levels via bisulfite sequencing might be a combination of 5hmC and 5mC levels since bisulfite sequencing can not distinguish between the two. This function can adjust 5mC levels of a bisulfite sequencing experiment if the user supplies corresponding 5hmC levels from the same sample.

Usage

adjust.methylC(mc,hmc)

Arguments

mc

a methylRawList or methylRaw containing 5mC levels of a sample or set of samples

hmc

a methylRawList or methylRaw containing 5hmC levels of a sample or set of samples. If a methylRawList given the sample order should be same as "mc" methylRawList object.

Value

returns adjusted 5-methyl cytosine levels in the form of methylRawList or methylRaw object depending on the input object

References

1. Booth, Branco, et al. (2012). Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution. Science, 934

2. Yu, Hon, et al. (2012). Base-resolution analysis of 5-hydroxymethylcytosine in the Mammalian genome. Cell, 149(6), 1368-80.

Examples

# NOT RUN {
# read 5hmC and 5mC files
hmc.file=system.file("extdata", "test1.myCpG.txt", package = "methylKit")
mc.file =system.file("extdata", "test2.myCpG.txt", package = "methylKit")

my5hmC=read( hmc.file,sample.id="hmc",assembly="hg18")
my5mC =read( mc.file,sample.id="mc",assembly="hg18")

# adjusting the 5mC levels using 5hmC levels
adjusted.5mC=adjust.methylC(my5mC,my5hmC)
# }