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

This function can compute the correlation of a pair of genes with Gini correlation and four other correlation methods. The signficance level (p-value) of computed correlation can be estimated with the permutation test method.

1 2 3 4 5 6 |

`idxvec` |
a numer vector containing two elements for the index of genes or samples in GEMatrix (e.g., c(1,2) ). |

`GEMatrix` |
a data matrix containing numeric variables. Example: rows correspond to genes and columns to samples. This parameter is the same as the "GEMatrix" defined for cor.matrix. |

`rowORcol` |
a character string ("row" or "col") indicating gene expression data will be extracted by rows or columns for correlation calculation. "row": correlation between two genes. "col": correlaiton between two samples. |

`cormethod` |
a character string that specifies the correlation method to be used for correlation calculation. |

`pernum` |
the number of permutation test used for calcluating statistical significance level (i.e., p-value) of correlations. |

`sigmethod` |
a character string ("two-sided" or "one-sided") specifying the method used to compute p-value for permutation test. |

A list with the following components:

`gcc.rankx ` |
a Gini correlation produced by using the rank information of the first gene (i.e., the first element in idxvec). |

`gcc.ranky ` |
a Gini correlation produced by using the rank information of the second gene (i.e., the second element in idxvec). |

`gcc.rankx.pvalue ` |
p-value of gcc.rankx. |

`gcc.ranky.pvalue ` |
p-value of gcc.ranky. |

`cor ` |
the correlation produced by "PCC", "SCC", "KCC" or "BiWt". |

`pvalue ` |
the p-value of cor. |

(1) To perform BiWt, the R package "biwt" should be installed in advance.

(2) When the cormethod is defined as "GCC", this function will output a list with four numeric elements: gcc.rankx, gcc.ranky, gcc.rankx.pvalue, gcc.ranky.pvalue. Otherwise, it will output a list with two elements (cor and p-value)

Chuang Ma, Xiangfeng Wang

`onegcc`

, `cor.matrix`

, `gcc.corfinal`

.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | ```
data(rsgcc) #load the sample data in rsgcc package
x <- rnaseq[1:4,] #construct a GEMatrix with the RNA-Seq data of the first four genes
#compute correlation between the 1st and 4th genes
corpair <- cor.pair(c(1,4), GEMatrix = x, rowORcol = "row",
cormethod = "GCC", pernum = 0,
sigmethod = "two.sided")
## Not run:
#compute correlation between the 1st and 4th genes,
#the p-value of correlation will be estimated with 2,000 permuation test.
corpair <- cor.pair(c(1,4), GEMatrix = x, rowORcol = "row",
cormethod = "GCC", pernum = 2000,
sigmethod = "two.sided")
#compute correlation between the 1st and 4th samples
corpair <- cor.pair(c(1,4), GEMatrix = x, rowORcol = "col",
cormethod = "GCC", pernum = 0,
sigmethod = "two.sided")
## End(Not run)
``` |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.