SNPhood (version 1.2.3)

testForAllelicBiases: Perform an allelic bias tests for each user region and bin.

Description

testForAllelicBiases performs tests for allelic biases for each binned user region using binomial tests. For the parameter readGroups, the name of exactly two read groups must be provided for which allelic ratio tests should be performed. See the Vignette for more details.

Usage

testForAllelicBiases(SNPhood.o, readGroups, confLevel = 0.95, nullHypothesisFraction = 0.5, calcBackgroundDistr = TRUE, nRepetitions = 100, pValuesToTestBackground = c(0.0001, 0.0005, 0.001, 0.005, seq(0.01, 1, 0.01)), verbose = TRUE)

Arguments

SNPhood.o

Object of class SNPhood

readGroups

Character or NULL. Default NULL. Read groups that should be plotted, specified by their name as obtained by the function annotationReadGroups). If set to NULL, all read groups will be considered.

confLevel

Numeric(1). Default 0.95. The confidence level for estimating the confidence intervals. Must be between 0 and 1.

nullHypothesisFraction

Numeric(1). Default 0.5. The expected probability under the null hypothesis of not having any bias. Must be between 0 and 1.

calcBackgroundDistr

Logical(1). Default TRUE. Should the background distribution be calculated? Note that this can be usually very time-consuming.

nRepetitions

Integer(1). Default 10. Number of repetitions for calculating the background distribution. Only relevant if calcBackgroundDistr is set to TRUE

pValuesToTestBackground

Numeric. Default c(0.0001, 0.0005, 0.001, 0.005, seq(0.01,1,0.01)). Set of p-values for which corresponding FDR values will be computed

verbose

Logical(1). Default TRUE. Should the verbose mode (i.e., diagnostic messages during execution of the script) be enabled?

Value

Object of class SNPhood with all the data from the allelic bias test stored in the slot additionalResults, which can be easily retrieved via the accessor function results. See the help pages of the result function (?results) or the vignette for details.

Examples

data(SNPhood.o, package="SNPhood")
## Perform the test without calculating the background distribution  
SNPhood.o = testForAllelicBiases (SNPhood.o, readGroups = c("paternal","maternal"))
str(results(SNPhood.o, type="allelicBias"), list.len = 8)
## Check the parameters
results(SNPhood.o, type="allelicBias", elements = "parameters")