RF Combine allows combining XML files from multiple experiments into a single profile.
For example, this can be useful when performing CIRS-seq experiments, to combine into a single profile both the reactivity of A/C residues probed with DMS, and of G/U residues probed with CMCT.
Alternatively, RF Combine is able to combine into a single profile multiple replicates of the same probing experiment. In these cases, the resulting XML files may contain optional “-error” tags, in which the per-base standard deviation of the measure from each experiment is reported.
When combining datasets containing NaN values, only non-NaN positions in all experiments will be combined, while the others will be reported as NaNs as well.
There is no limit to the number of experiments that RF Combine can handle. It can be used both on individual XML files, or on whole XML folders generated by either RF Norm or RF ModCall.
RF Combine further allows retaining only transcripts whose Pearson correlation coefficient exceeds a user-defined threshold.

Usage

To list the required parameters, simply type:

$ rf-combine -h

Parameter	Type	Description
-p or --processors	int	Number of processors (threads) to use (Default: 1)
-o or --output-dir	string	Output directory for writing combined data in XML format (Default: combined/)
-ow or --overwrite		Overwrites the output directory if already exists
-s or --stdev		When combining multiple replicates, an optional "-error" tag will be reported in the output XML files, containing the per-base standard deviation of the measure
-d or --decimals	int	Number of decimals for reporting reactivities (1-10, Default: 3)
-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
-c or --min-correlation	float	Minimum correlation to report a combined profile (-1<r<1, Default: off) Note: if more than two replicates are being combined, RF Combine requires this threshold to be satisfied all pairwise comparisons
-S or --spearman		Uses Spearman instead of Pearson to calculate correlation
-l or --log-transform		Log transforms reactivity values before averaging
-i or --ignore-NaNs		NaNs are ignored when calculating mean reactivities Note: this parameter enables combining XML files from experiments with different sets of reactive bases (e.g., A/C and G/U)