calcMW

sequence

 One of "5OH" (default), "5PPP-3P", or "5PPP-3OH" describing 5' and/or 3' modifications of the fragment

extra

 One of 'Na', 'K', or '' (default) specifying whether or not the molecular weight should be calculated for a salt adduct 

adduct

 One of 'T' or 'C' indicating which cleavage reaction is employed to generate the fragment 


  Function to calculate molecular weight of a fragment generated by the MassCLEAVE assay for either the T or C cleavage reactions


 character 

 arith 

This package is designed for the import, quality control, analysis, and visualization of methylation data generated using Sequenom's MassArray platform.  The tools herein contain a highly detailed amplicon prediction for optimal assay design.  Also included are quality control measures of data, such as primer dimer and bisulfite conversion efficiency estimation.  Methylation data are calculated using the same algorithms contained in the EpiTyper software package.  Additionally, automatic SNP-detection can be used to flag potentially confounded data from specific CG sites.  Visualization includes barplots of methylation data as well as UCSC Genome Browser-compatible BED tracks.  Multiple assays can be positionally combined for integrated analysis.

Reid F Thompson

MassArray

Analytical Tools for MassArray Data

calcMW function

One of "5OH" (default), "5PPP-3P", or "5PPP-3OH" describing 5' and/or 3' modifications of the fragment

One of 'Na', 'K', or '' (default) specifying whether or not the molecular weight should be calculated for a salt adduct

One of 'T' or 'C' indicating which cleavage reaction is employed to generate the fragment

Function to calculate molecular weight of a fragment generated by the MassCLEAVE assay for either the T or C cleavage reactions

calcMW: Calculate molecular weight

Description

Usage

Arguments

Value

Examples