replicatesSpearmancor {RNAither} | R Documentation |
Computes Spearman's rank correlation coefficient for each replicate - either inside each experiment, or between experiments.
replicatesSpearmancor(header, dataset, flag, col4val, col4anno, fileNameSuffix)
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. |
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.
data(exampleHeader, package="RNAither") data(exampleDataset, package="RNAither") replicatesSpearmancor(header, dataset, 1, "SigIntensity", "GeneName", "testfile1_")