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charm (version 2.18.0)

Analysis of DNA methylation data from CHARM microarrays

Description

This package implements analysis tools for DNA methylation data generated using Nimblegen microarrays and the McrBC protocol. It finds differentially methylated regions between samples, calculates percentage methylation estimates and includes array quality assessment tools.

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Version

Version

2.18.0

License

LGPL (>= 2)

Maintainer

Last Published

February 15th, 2017

Functions in charm (2.18.0)

Calculate FDR q-values for differentially methylated regions (DMRs)

Obtain False Discovery Rate q-values for the DMR candidates returned by dmrFind.

Estimate percentage DNA methylation from log-ratios

Correct spatial artifacts

Count probe GC content

Get CpG density for genomic regions

Find differentially methylated regions (DMRs)

normalizeBetweenSamples

Between-sample normalization

Plot user-provided regions.

Estimate DNA methylation

Given two data frames with columns "chr", "start", and "end", identify the nearest region in one to the other.

Plot differentially methylated regions (DMRs) found using the dmrFind function.

Redefine array regions given chromosomal coordinates.

Plot differentially methylated regions (DMRs) found using the dmrFinder function.

Read in McrBC/CHARM DNA methylation microarray data

Log-ratio density plot for all probes and control probes

Identify DMR candidates using a regression-based approach and correcting for batch effects.

Validate a sample description file for two-color microarray data

getControlIndex

Get indices of control probes from CpG-free regions

Classical multi-dimensional scaling plot of charm data.

normalizeWithinSamples

Within-sample normalization for two-color data

Plot user-supplied genomic regions using data returned by the dmrFinder function.

Calculate probe quality scores

Remove background

Boxplots of control and non-control probes

Find the mode of a density function

Microarray quality report