getPatternCC: getPatternCC
In cbtolson/classSNitch: Classifies RNA Structure Change in Chemical Mapping Data

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

A function to get the correlation coefficient between SHAPE trace change patterns.

1	getPatternCC(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 value to which the samples are to be compared (e.g. a wild type 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.

The pattern for a single SHAPE reacitivity trace is the pattern of increase in reactivity or decrease in reactivity between nucleotides. If the change is less than the tolerance value, it is considered a none change. The pattern change value is the Pearson correlation coefficient between the base vector pattern and the pattern of each row (or column) in sample.

A numeric vector of pattern correlation coefficients.

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 pattern correlation coefficient
pat = getPatternCC(samp_nreduce)