RF Correlate allows calculating pairwise Pearson correlations of structure probing experiments. It can be invoked either on individual transcripts or on whole XML folders.
Overall, as well as per-transcript correlations are reported in CSV format.
To list the required parameters, simply type:
$ rf-correlate -h
|-p or --processors||int||Number of processors to use (Default: 1)|
|-o or --output||string||Output CSV file (Default: rf_correlate.csv)|
|-ow or --overwrite||Overwrites output file (if the specified file already exists)|
|-m or --min-values||float||Minimum number of values to calculate correlation (Default: off)
Note: if a value between 0 and 1 is provided, this is interpreted as a fraction of the transcript's length
|-s or --skip-overall||Skips overall experiment correlation calculation (faster)|
--min-values specified value is interpreted as a fraction of the transcript's length, only reactive bases (specified by the XML
reactive attribute; for additional details, please refer to the RF Norm documentation) are considered. For example, if a transcript containing 25% of each base has been modified with DMS (than only modifies A/C residues), setting
--min-values to 0.5 will cause RF Correlate to skip the transcript if more than 50% of the A/C residues are NaNs.