getMagCC: getMagCC
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 correlation coefficient between SHAPE trace magnitudes.

1	getMagCC(sample, base=sample[1,], margin=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.

This function calculates the Pearson correlation coefficient between the base vector and each row (or column) in sample.

A numeric vector of 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 magnitude correlation coefficient
mag = getMagCC(samp_nreduce)