Methmean_site: Calculate the methylation mean for cytosine sites.
In xiaowangCN/GeneDMRs: GeneDMRs: an R package for Gene-based differentially methylated regions analysis
View source: R/Methmean_match.R
Methmean_site R Documentation
Calculate the methylation mean for cytosine sites.
Description
This function outputs the methylation mean for each cytosine site. It will calculate methylation difference along each group.
Formula:The mean methylation of a cytosine of one treatment group was calculated by:
E((E[MR]_i )/(E[TR]_i ))*W_i and W_i = (E[TR]_i )/(EE[TR]_i ),
where [MR]_i and [TR]_i are methylated and total reads number of the CpG,
n is the total individual number of one treatment group, and
W_i is the weight of reads of the CpG of individual i.
Usage
Methmean_site(inputmethfile_QC)
Arguments
inputmethfile_QC
refers to the input of methylation file after quality control.
Value
Outputs a data frame of the methylation mean of provided cytosine sites.
Examples
siteall <- Methmean_site(inputmethfile_QC)
xiaowangCN/GeneDMRs documentation built on Nov. 22, 2023, 11:19 p.m.
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View source: R/Methmean_match.R
| Methmean_site | R Documentation |
Calculate the methylation mean for cytosine sites.
Description
This function outputs the methylation mean for each cytosine site. It will calculate methylation difference along each group.
Formula:The mean methylation of a cytosine of one treatment group was calculated by: E((E[MR]_i )/(E[TR]_i ))*W_i and W_i = (E[TR]_i )/(EE[TR]_i ), where [MR]_i and [TR]_i are methylated and total reads number of the CpG, n is the total individual number of one treatment group, and W_i is the weight of reads of the CpG of individual i.
Usage
Methmean_site(inputmethfile_QC)
Arguments
inputmethfile_QC |
refers to the input of methylation file after quality control. |
Value
Outputs a data frame of the methylation mean of provided cytosine sites.
Examples
siteall <- Methmean_site(inputmethfile_QC)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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