wiggle_smooth: Sliding window smooth of wiggle data
In luisvalesilva/hwglabr: Collection of R functions used in the Hochwagen Lab

Description Usage Arguments Value Examples

This function allows you to smooth wiggle data using a sliding window.

1	wiggle_smooth(wiggleData, chrNumber, bandwidth = 200, useKsmooth = FALSE)

`wiggleData`	Accepts input in one of the following formats: An R list of the 16 chromosome wiggle data (output of `readall_tab()`). An element of an R list of the form described in the first item above. Can be extracted with either '[]' or '[[]]'. An R data frame in the same format as the individual chromosome data frames composing the list described in the first item above. No default.
`chrNumber`	An integer representing the chromosome to smooth. Will be ignored in case the provided `wiggleData` is not a list of data for the 16 chromosomes. No default.
`bandwidth`	An integer representing the length of the smoothing window in bp (or the Gaussian kernel bandwith, if `useKsmooth = TRUE`). Defaults to `200`.
`useKsmooth`	Boolean indicating choice of smoothing function: `useKsmooth = FALSE`: use a simple sliding window smoother. Smoothing is performed by sliding a window of the specified size (`bandwidth` argument) over all genomic positions in the data and replacing the position values by the middle position and the signal values by their mean. `useKsmooth = TRUE`: use a Gaussian Kernel Regression Smoother. Smoothing is performed using function `ksmooth()` from 'stats' package using the default `normal` kernel and the specified bandwith. Defaults to `FALSE`.

An R data frame with two columns: genome position and smoothed signal.

## Not run: 
wiggle_smooth(WT, 1, 200)

wiggle_smooth(rec8, 16, 100)

wiggle_smooth(WT[[5]], bandwidth = 1000)

wiggle_smooth(WT[[9]], bandwidth = 1000, useKsmooth = T)

## End(Not run)