# detect.spikes: Detects spikes in series of numbers. In peakPick: Peak Picking Methods Inspired by Biological Data

## Description

This algorithm detects spikes rising above a user-specified number of standard deviations numbers in a certain window. Use this algorithm to detect short spikes rather than smooth bumps in series of numbers. Please refer to the paper by Weber et al. for more details.

## Usage

 ```1 2``` ```detect.spikes(mat, roi, winlen, spike.min.sd = 3, mc.cores = 1, verbose = FALSE) ```

## Arguments

 `mat` matrix of series with series organized columnwise. The algorithm treats each column separately. `roi` vector of two integers (c(min, max)) defining positions in all series (rows in mat) to consider for spike detection, used together with winlen. Must lie within the interval [2, nrow(mat) - 1]. Will be coerced to integers. `winlen` integer defining the window of positions to consider for mean and sem estimation for each series. Each estimation limits itself to the position and a plus/minus winlen positions large window. Thus, winlen must not be chosen larger than that the windows fit within mat, given the roi. I.e. roi[1] - winlen >=1 AND roi[length(roi)] + winlen <= nrow(mat). Will be coerced to an integer. `spike.min.sd` numeric minimum number of standard deviations for a spike to rise above the mean in order to be considered for a spike call and to be excluded from the mean estimation of each subsequent iteration of the spike calling algorithm `mc.cores` the number of cores do perform this calculation `verbose` Boolean indicating the number of new peaks detected with each iteration. The algorithm stops as soon as this number does not sink anymore. Turn this on if running into problems.

## Value

boolean matrix corresponding to mat, representing spike positions.

## References

Weber, C.M., Ramachandran, S., and Henikoff, S. (2014). Nucleosomes are context-specific, H2A.Z-modulated barriers to RNA polymerase. Molecular Cell 53, 819-830.

peakPick documentation built on May 2, 2019, 7:02 a.m.