SequenceSlotting: Sequence Slotting

In BlasBenito/IgnexCompare:

Description

It takes as inputs two pollen sequences produced by the function PrepareInputSequences, and computes the best slotting.

Arguments

sequences	A list produced by the function PrepareInputSequences or DistanceMatrix
compute.p.value	Boolean. Use TRUE to compute p-values via distance matrix randomization.
method	Either "manhattan" computed as sum(abs(x - y)), "hellinger" computed as sqrt(1/2 * sum(sqrt(x)-sqrt(y))^2), or "euclidean", computed as sqrt(sum((x - y)^2)).
silent	Boolean. Use TRUE to remove all messages.
diagonal	Boolean. TRUE to compute the sequence slotting using diagonals (true shortest path). FALSE to compute the sequence slotting without considering diagonals. Using diagonals produces lower psi values but better alignments between sequences.

Author(s)

Blas Benito <[e-mail]>

Examples

#generating random input data
results.table=GenerateResultsTable(10)
str(results.table)

BlasBenito/IgnexCompare documentation built on June 9, 2019, 2:53 a.m.