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

This function tests if a pathway (or gene set) consists of any protein (or gene) that shows different mean abundance (or expression) between two groups of samples.

1 | ```
RHT.2samp(path.idx, datX, datY, nsim = 1000, seed = 123)
``` |

`path.idx` |
This is a LIST. Each element in the list contains the indice of proteins (or genes) for a pathway in the data set. |

`datX` |
An N1 by p matrix of protein abundance (or gene expression) from one group of samples. Each row represents one sample and each column represents a protein (or a gene). |

`datY` |
An N2 by p matrix of protein abundance (or gene expression) from another group of samples. Each row represents one sample and each column represents a protein (or a gene). |

`nsim` |
Number of resamples needed to calculate the p-value. By default, nsim=1000. |

`seed` |
A single integer that controls the random number generator in the resampling. |

The function returns the p-values for each pathway in the list `path.idx`

.

Lin S. Chen and Pei Wang

Chen LS, Paul D, Prentice RL and Wang P. (2011) A regularized Hotelling's T-square test for pathway analysis in proteomics studies. Journal of the American Statistical Association, in press.

See Also `RHT.fun`

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | ```
## We simulate a data set X with N=10 samples and p=50 proteins,
## and a second data set Y with N=8 sample and the same number of proteins.
## 20% of the data are missing.
set.seed(1)
X <- matrix(rnorm(500),nrow=10)
X[sample(1:500, 0.2*500)] <- NA
Y <- matrix(rnorm(400),nrow=8)
Y[sample(1:400, 0.2*400)] <- NA
## Among the 50 proteins, we randomly assign 2 pathways, with 5 and 12 proteins, respectively.
path.idx <- list()
path.idx[[1]] <- 1:5
path.idx[[2]] <- 13:24
names(path.idx) <- c("pathway A", "pathway B")
## The following function tests each pathway to see
## if any of the proteins in each pathway shows different
## abundance/expression between data X and Y.
pval <- RHT.2samp(path.idx, datX=X, datY=Y)
``` |

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