Description Usage Arguments Details Author(s)
View source: R/methStatusEval.R
Classify a locus as either 'methylation-susceptible locus' (MSL) or 'non-methylated locus' (NML). See Details.
1 | methStatusEval(x, error=0.05, uninformative=TRUE)
|
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) |
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).
Andres Perez-Figueroa (anpefi@uvigo.es)
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