replicatesSpearmancor {RNAither} | R Documentation

## Compute the correlation coefficient betwenn replicates or experiments

### Description

Computes Spearman's rank correlation coefficient for each replicate - either inside each experiment, or between experiments.

### Usage

    replicatesSpearmancor(header, dataset, flag, col4val, col4anno, fileNameSuffix)

### Arguments

`header` | the header of a dataset file generated with `generateDatasetFile`
`dataset` | an R data frame generated with `generateDatasetFile`
`flag` | 1 or 2. 1 will compute the coefficient for a maximum of 3 replicates, for each experiment available in the dataset. 2 will summarize the replicates from each experiment with their root mean square and compute the correlation coefficient between experiments.
`col4val` | a character string specifying the column whose values will be used to compute the correlation coefficient
`col4anno` | a character string specifying the name of the dataset column to be used to define the replicate, e.g. `"GeneName"` or `"Internal_GeneID"`
`fileNameSuffix` | a character string that will be used to name the output file containing a table with the correlation coefficients.

### Value

For `flag==1`, the correlation coefficients are printed out to the shell and saved in a text file named after the experiment name specified in the header concatenated with the character string filenamesuffix and "Spearmancor.txt".

For `flag==2`, the correlation coefficients are printed out to the shell and saved in a text file named after the experiment name specified in the header concatenated with the character string filenamesuffix and "Spearmancor\_AllExp.txt".

The function returns a table containing the correlation coefficients.

### Examples

    data(exampleHeader, package="RNAither")
    data(exampleDataset, package="RNAither")

    replicatesSpearmancor(header, dataset, 1, "SigIntensity", "GeneName", "testfile1_")

[Package RNAither version 2.36.0 Index]