Description Usage Arguments Value Examples

`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.

1 2 3 4 | ```
testForAllelicBiases(SNPhood.o, readGroups, confLevel = 0.95,
nullHypothesisFraction = 0.5, calcBackgroundDistr = TRUE,
nRepetitions = 100, pValuesToTestBackground = c(1e-04, 5e-04, 0.001,
0.005, seq(0.01, 1, 0.01)), verbose = TRUE)
``` |

`SNPhood.o` |
Object of class |

`readGroups` |
Character or NULL. Default NULL. Read groups that should be plotted, specified by their name as obtained by the function |

`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 |

`nRepetitions` |
Integer(1). Default 10. Number of repetitions for calculating the background distribution.
Only relevant if |

`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? |

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.

1 2 3 4 5 6 | ```
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")
``` |

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