Description Usage Arguments Details Value Author(s) References See Also Examples

Perform an intra-experiment analysis in conjunction with any of the classical hypothesis testing methods, such as t-test, Wilcoxon test, etc.

1 2 | ```
intraAnalysisClassic(x, y = NULL, splitSize = 5, metaMethod = addCLT,
func = t.test, p.value = "p.value", ...)
``` |

`x` |
a numeric vector of data values |

`y` |
an optional numeric vector of values |

`splitSize` |
the minimum number of size in each split sample. splitSize should be at least 3. By default, splitSize=5 |

`metaMethod` |
the method used to combine p-values. This should be one of addCLT (additive method [1]), fishersMethod (Fisher's method [5]), stoufferMethod (Stouffer's method [6]), max (maxP method [7]), or min (minP method [8]) |

`func` |
the name of the hypothesis test. By default func=t.test |

`p.value` |
the component that returns the p-value after performing
the test provided by the |

`...` |
additional parameters for |

This function performs an intra-experiment analysis for the given
sample(s) [1]. Given x as the numeric vector, this function first splits x
into smaller samples with size *splitSize*, performs hypothesis
testing using *func*, and then combines the p-values
using *metaMethod*

intra-experiment p-value

Tin Nguyen and Sorin Draghici

[1] T. Nguyen, R. Tagett, M. Donato, C. Mitrea, and S. Draghici. A novel bi-level meta-analysis approach – applied to biological pathway analysis. Bioinformatics, 32(3):409-416, 2016.

`bilevelAnalysisClassic`

, `intraAnalysisGene`

, `bilevelAnalysisGene`

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | ```
set.seed(1)
x <- rnorm(10, mean = 0)
# p-value obtained from a one-sample t-test
t.test(x, mu=1, alternative = "less")$p.value
# p-value obtained from an intra-experiment analysis
intraAnalysisClassic(x, func=t.test, mu=1, alternative = "less")
# p-value obtained from a one-sample wilcoxon test
wilcox.test(x, mu=1, alternative = "less")$p.value
# p-value obtained from an intra-experiment analysis
intraAnalysisClassic(x, func=wilcox.test, mu=1, alternative = "less")
set.seed(1)
x <- rnorm(20, mean=0); y <- rnorm(20, mean=1)
# p-value obtained from a two-sample t-test
t.test(x,y,alternative="less")$p.value
# p-value obtained from an intra-experiment analysis
intraAnalysisClassic(x, y, func=t.test, alternative = "less")
# p-value obtained from a two-sample wilcoxon test
wilcox.test(x,y,alternative="less")$p.value
# p-value obtained from an intra-experiment analysis
intraAnalysisClassic(x, y, func=wilcox.test, alternative = "less")
``` |

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