plotAndSummarizeAllelicBiasTest {SNPhood} | R Documentation |
plotAndSummarizeAllelicBiasTest
summarizes the allelic bias test across SNP regions and bins by calculating various summary statistics.
See the Vignette for more details. TODO
plotAndSummarizeAllelicBiasTest(SNPhood.o, signThreshold = 0.05, fileToPlot = NULL)
SNPhood.o |
Object of class |
signThreshold |
Numeric(1). Default 0.05. The significance threshold (such as p-value or FDR threshold). Must be between 0 and 1. If the parameter belongs to a plotting function, a horizontal line is drawn at the chosen value. For the allelic bias summary plots, p-values below this threshold and the corresponding allelic fractions are highlighted. |
fileToPlot |
Character(1) or |
A named list with various elements, each of which summarizes the allelic bias tests with a different focus. TODO
data(SNPhood, package="SNPhood") SNPhood.o = testForAllelicBiases (SNPhood.o, readGroups = c("maternal", "paternal")) SNPhood.o = plotAndSummarizeAllelicBiasTest(SNPhood.o)