Compute correlation between miRNA and gene/transcript expression.

Version | 1.2 |
---|---|

Bundle | sequencing |

Categories | smallRNA Expression Integration |

Authors | Ping Chen (ping.chen@helsinki.fi), Katherine Icay (katherine.icay@helsinki.fi) |

Issue tracker | View/Report issues |

Requires | R |

Source files | component.xml GlobalCorrelation.R |

Usage | Example with default values |

Name | Type | Mandatory | Description |
---|---|---|---|

gene | CSV | Mandatory | Gene expression matrix. |

mirna | CSV | Mandatory | miRNA expression matrix. |

Name | Type | Description |
---|---|---|

correlated_filtered | CSV | CSV file containing correlated miRNA-mRNA pairs within cutoff values and with `minSample` . |

correlated_all | CSV | CSV file containing all correlated miRNA-mRNA pairs with `minSample` . |

expression_miRNA | CSV | Filtered expression matrix of miRNAs in `correlated_filtered` . |

expression_mRNA | CSV | Filtered expression matrix of mRNAs in `correlated_filtered` . |

Name | Type | Default | Description |
---|---|---|---|

cutoff | float | 0.4 | The absolute threshold defining the most interesting miRNA-mRNA pairs. If `cutoffType="correlation"` , both positively and negatively correlated pairs will appear. If `pvalue` is chosen, only those values less than or equal to the cutoff will apear. |

cutoffType | string | "correlation" | The type of cutoff. Values are either `correlation (corr)` or `pavalue (pval)` . |

hasNA | boolean | false | A boolean defines if there is missing value in the input expression data. |

method | string | "pearson" | a character string indicating which correlation coefficient
(or covariance) is to be computed. One of `pearson`
(default), `kendall` , or `spearman` , can be abbreviated. |

minSample | int | 1 | The minimum number of samples. Samples with missing values will be removed when computing correlation. It defines the minimum number of samples required for correlation analysis. |

Test case | Parameters▼ | IN gene |
IN mirna |
OUT correlated_filtered |
OUT correlated_all |
OUT expression_miRNA |
OUT expression_mRNA |
---|---|---|---|---|---|---|---|

case1 | (missing) | gene | mirna | correlated_filtered | correlated_all | expression_miRNA | expression_mRNA |

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