Up: Component summary
Up: Component summary
Component
GlobalCorrelationCompute 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 |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| gene | CSV | Mandatory | Gene expression matrix. |
| mirna | CSV | Mandatory | miRNA expression matrix. |
Outputs| 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. |
Parameters| 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 cases| 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 |