contained_asymmetries

This function performs strand asymmetry estimation of strand-assigned nucleotide-sequence motifs within strand-assigned regions.

Required inputs:

Argument	Explanation
regions	One or more BED-formatted files, containing the regions within which to estimate motif asymmetries.
motifs	One or more BED-formatted files, for each of which the asymmetries are calculated.

Optional inputs:

Argument	Explanation
–names_regions	Assign a name for each of the BED-formatted region files to allow for more human readable output.
–names_motifs	Assign a name for each of the BED-formatted motif files to allow for more human readable output.
–orientation_region	Orient file(s) relative to annotated BED-formated region file(s) and perform the analysis for the un-annoated file with the new annotations.
–orientation_motif	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 regions and the motifs regarding same or opposite strand orientation. Default is 0.5.
–expected_asym_conv_div	The expected convergent / divergent asymmetry bias between the regions and the motifs. Default is 0.5.
–score	Optional flag. If provided, assumes the last column of the region files is a scoring metric and uses it to subdivide the analysis into bins.
–bins_score	Number of bins to subdivide the score column into. Only runs when –score is provided. Default value is 10.
–plots	Returns the associated plots of the asymmetries for each file.

Outputs:

• Table containing strand asymmetries of for same strand and opposite strand orientations, p-value, p-value with Bonferoni correction.

• Barplot of strand asymmetries for each pair of comparisons.

• Barplot of strand-asymmetries across the score quantiles.

• Table of strand asymmetries for same / opposite and convergent / divergent asymmetries per bin, associated p-vaues and p-values Bonferoni correction.

Note

The results from files consisting of palindromic motifs will not show strand asymmetries.