msap (version 1.1.8)

methStatusEval: classify a locus as either MSL or NML.

Description

Classify a locus as either 'methylation-susceptible locus' (MSL) or 'non-methylated locus' (NML). See Details.

Usage

methStatusEval(x, error=0.05, uninformative=TRUE)

Arguments

x

A list of mixed band patterns for a given fragment across all the samples. Values of 11, 10, 1 and 0 represent patterns HPA+/MSP+,HPA+/MSP-,HPA-/MSP+,HPA-/MSP-, respectively.

error

Repeatibility value of MSAP assays. It provides a threshold to consider methylation events as genotyping errors.

uninformative

A logic value determining how to deal with HPA-/MSP- pattern. FALSE indicates that HPA-/MSP- stands for hypermethylated target (ignoring genetic mutation), and TRUE (default) stands for uninformative pattern (as this could be caused by genetic mutation or hypermethylation)

Details

Individual fragments (loci) are classified as 'methylation-susceptible loci' (MSL) or 'non-methylated loci' (NML), depending on whether the observed proportion of discordant HPA/MSP scores suggestive of methylation(i.e. number of individuals with contrastinf HPA/MSP scores for the fragment divided by the total number of individuals assayed) exceeded a user-defined threshold (0.05 by default).