pairwise_asymmetries¶

This function performs strand asymmetry estimation between two strand-assigned motifs in proximity or overlapping each other.

**Required inputs:**¶
Argument	Explanation
motifsA	One or more BED-formatted files
motifsB	One or more BED-formatted files

**Optional inputs:**¶
Argument	Explanation
–names_A	The name of each of the inputted BED-formatted motif A files.
–names_B	The name of each of the inputted BED-formatted motif B files.
–upstream_only	Only look for occurrences of motif A upstream of motif B. Incompattible with -downstream.
–downstream_only	Only look for occurrences of motif A downstream of motif B. Incompatible with -upstream.
–orientation	Orient file(s) relative to annotated BED-formated motif file(s) and perform the analysis for the un-annoated file with the new annotations.
–expected_asym	The expected asymmetry bias between the pairs of motifs regarding same or opposite strand orientation. Default is 0.5.
–expected_asym_conv_div	The expected convergent / divergent asymmetry bias between the pairs of motifs. Default is 0.5.
–min_distance	Minimum distance to consider in the analysis. Default is 0.
–max_distance	Maximum distance to consider in the analysis. Default is 100.
—bins	Number of bins to subdivide the analysis in. Default is 1, which does not perform this analysis.
--plots	Returns the associated plots of the asymmetries for each file.

Outputs:

Table containing strand asymmetries of ++/+-/-+/– orientations, same-strand, opposite strand, p-value, p-value with Binomial correction (corrected for multiple file queries).
Barplots of strand asymmetries for each pair of comparisons for same versus opposite and convergent versus divergent strand orientations.
Barplot of strand-asymmetries across the bins for same versus opposite and convergent versus divergent strand orientations.

Note

The results from files consisting of palindromic motifs will not show strand asymmetries.
The identification of the closest element is performed relative to elements of the first file provided and the results are influenced by the order of the input files.