getChangeVar: getChangeVar

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

Description

A function to get the spread or variance of change for a SHAPE trace.

Usage

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

Arguments

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.

Details

This function calculates the variance of change positions for each row (or column) in sample.

Value

A numeric vector of trace change variances.

Author(s)

Chanin Tolson

See Also

getFeatures

Examples

#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 change variance
cv = getChangeVar(samp_nreduce)

cbtolson/classSNitch documentation built on May 13, 2019, 2:14 p.m.