analyzeSequenom {RSeqMeth}R Documentation

Calculates methylation ratios and proportions

Description

The user is interactively asked to specify

Usage

analyzeSequenom(matchedName = NA, methName = NA, seqNames = NA, cull=TRUE, 
  writeOut = TRUE, quiet = FALSE, minMass = 1500, maxMass = 7000)

Arguments

matchedName Name of the file to read the matched peak data from - if left to default then the user is asked to interactively choose the matched peaks table.
methName If cull is TRUE then the name of the file to read methylation grid data from - if left to default then the user is asked to interactively choose the methylation grid data. If cull is FALSE this value is ignored.
seqNames A character vector of file names to read sequences from. The sequences are specified in the same order that their amplicons appear in the matched peaks table. If left to default then the user is asked to interactively choose the sequence files used in analysis.
cull logical: if TRUE (default) then methylation grid data will be read from methName and missing values from this grid will be used to cull methylation ratios that did not meet the EpiTyper Probability Threshold setting at the time the methylation grid was exported. if FALSE no culling will occur and the value of methName is ignored.
writeOut logical: if TRUE (default) then the calculated methylation values are writted to tab separated text files in the same directory as matchedName. Two files are written:

<matchedName> Weighted - contains for each informative CpGUnit (excluding overlaps) the methylation ratio calculated using the weighted formula.

<matchedName> Proportion - contains for each informative CpGUnits (including overlaps) the proportion of each peak eg (0/2 CpGs methylated, 1/2 CpGs methylated, 2/2 CpGs methylated)

quiet logical: if FALSE no output is written to the screen
minMass The minimal mass of a peak to be included in the analysis.
maxMass The maximal mass of a peak to be included in the analysis.

Details

Currently, only T cleavage data is interpreted. Matched peak files containing C cleavage data have not been tested.

Value

A list containing three elements:

Sequenom - Reproduces the calculations made by EpiTyper.

Weighted - Ratio for each CpGUnits (excluding overlaps) calculated using the weighted formula.

Proportion - Proportion for each peak in each informative CpGUnit (including overlaps.

Each of these is a list which contains an element for each amplicon in the input matched peaks table. Each of these amplicon elements contains two elements:

Name - The name of the amplicon as specified in the matched peaks table.

Ratios - A data frame containing for each sample in the matched peaks table the methylation ratio or proportion as given above.

Author(s)

Aaron Statham

References

Coolen MW, Statham AL, Gardiner-Garden M, Clark SJ. (2007) Nucleic Acids Research 35(18):e119 Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements.

See Also

ampliconReport

Examples

## run completely interactively, everything obtained from the user
#meth <- analyzeSequenom()

## specified matched peaks table, do not cull, sequences will be specified
## interactively by the user
#meth <- analyzeSequenom(matchedName = "Plate1 matched.txt", cull=FALSE)

## runs completely without user intervention - output is not written to files
#meth <- analyzeSequenom(matchedName = "Plate1 matched.txt", cull=FALSE, seqNames 
#= c("EN1.txt", "EN1.txt", "SCTR.txt", "SCTR.txt"), quiet=TRUE, writeOut=FALSE)


[Package RSeqMeth version 1.0.2 Index]