tryAllMotifAlignments: Try all motif alignments and return max score
In PWMEnrich: PWM enrichment analysis

This function tries all offsets of motif1 compared to motif2 and returns the maximal (unnormalized) correlation score.

1	tryAllMotifAlignments(m1, m2, min.align = 2, exclude.zero = FALSE)

`m1`	frequency matrix of motif 1
`m2`	frequency matrix of motif 2
`min.align`	minimal number of basepairs that need to align
`exclude.zero`	if to exclude offset=0, useful for calculating self-similarity

The correlation score is essentially the sum of correlations of individual aligned columns as described in Pietrokovski (1996).

single maximal score

Pietrokovski S. Searching databases of conserved sequence regions by aligning protein multiple-alignments. Nucleic Acids Res 1996;24:3836-3845.

PWMEnrich documentation built on Nov. 8, 2020, 7:45 p.m.

PWMEnrich index

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