getContiguous: getContiguous
In classSNitch: Classifies RNA Structure Change in Chemical Mapping Data

Description Usage Arguments Details Value Author(s) See Also Examples

A function to get the number of stretches of contiguous change.

1	getContiguous(sample, base=sample[1,], margin=1, tol=0.1)

`sample`	A numeric matrix containing values to be compared (e.g. a set of mutant SHAPE traces).
`base`	An optional numeric vector containing the values to which the samples are to be compared (e.g. a wildtype SHAPE trace). Default is the first trace in sample.
`margin`	An optional number indicating if the samples are organized by rows or columns, where 1 indicates rows and 2 indicates columns. Default is 1.
`tol`	An optional number indicating the tolerance for the change. Default is 0.1.

This function calculates the number of stretches of contiguous change between the base vector and each row (or column) in sample.

A numeric vector of counts

Chanin Tolson

getFeatures

#sample data
sample = matrix(sample(1:100), ncol=10)
#normalize
samp_norm = normalize(sample)
#reduce noise
samp_nreduce = reduceNoise(samp_norm, trim=1, high=4)
#get trace difference
contig = getContiguous(samp_norm)