AnalysisRegionResults: AnalysisRegionResults instances

Description

AnalysisResults heir with the analyses performed in a range of the whole genome.

Usage

analysisRegionResults(analysisResults, set, range, snpspvals = data.frame(), regionlm = list(), relevantsnps = character(), snpsVar = as.numeric(NA), equation = NULL, nperm = 1e+05)
"getRange"(object)
"getRDA"(object)
"globalPval"(object)
"globalR2"(object)
"regionLM"(object)
"RDAPval"(object)
"regionR2"(object)
"snps"(object)
"snpsPvals"(object)
"snpsVar"(object)
"plotRDA"(object, n_feat = 5)
"plotRegionR2"(object, feat, ...)
"topRDAhits"(object, pval = 0.05)

Arguments

analysisResults

AnalysisResults

set

MethylationSet or ExpressionSet

range

GenomicRanges

snpspvals

Data.frame obtained from calculateRelevantSNPs

regionlm

Data.frame obtained from explainedVariance

relevantsnps

Character vector with the relevant snps names

snpsVar

Numeric with the variability of the SNP matrix explained by the components used to adjust the linear model.

equation

Character containing the formula to be used to create the model.

nperm

Numeric with the number of permutations used to compute RDAs p-values.

object

MethylationResults

n_feat

Numeric with the number of features to be highlighted.

feat

Numeric with the index of the cpg or character with its name.

...

Further arguments passed to plotLM

pval

numeric with the p-value threshold. Only features with a p-values below this threshold will be shown.

Value

An AnalysisRegionResults

Methods (by generic)

getRange: Get range where the analyses was performed
getRDA: Get rda object.
globalPval: Get global p-value.
globalR2: Get global R2.
regionLM: Get R2 values of cpgs vs variables.
RDAPval: Get p-value of RDA.
regionR2: Get R2 of the region vs variables lineal model
snps: Get SNPs data
snpsPvals: Get p-values of correlations of snps-cpgs pairs
snpsVar: Get variance of SNP matrix present in the component used to adjusting.
plotRDA: Plot RDA results
plotRegionR2: Plot R2 region values
topRDAhits: Get the top features associated with the RDA

Slots

range: GenomicRanges used to perform the analysis.
snps: Character vector with the snps that are correlated to at least one cpg.
snpsPvals: Data.frame with the results of the correlation test SNP-cpg.
snpsVar: Numeric with the variability of the SNP matrix explained by the components used to adjust the linear model.
rda: rda object from vegan package with the results of RDA analysis in the range.
regionLM: List with the R2 of the linear model of beta values against our variable of interest and against significant SNPs for each cpg.
regionR2: Numeric with the R2 of the region calculated using a redundancy analysis.
RDAPval: Numeric with the p-value of the RDA.
globalR2: Numeric with the global R2.
globalPval: Numeric with the probability of finding a region with the same number of probes with a bigger R2.

Examples

Run this code

showClass("AnalysisRegionResults")

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