62 lines
1.6 KiB
Plaintext
62 lines
1.6 KiB
Plaintext
---
|
|
title: "Rle Tips and Tricks"
|
|
author:
|
|
- name: "Patrick Aboyoun"
|
|
- name: "Beryl Kanali"
|
|
affiliation: "Converted 'RleTricks' vignette from Sweave to RMarkdown."
|
|
date: "`r format(Sys.time(), '%d %B, %Y')`"
|
|
package: S4Vectors
|
|
vignette: >
|
|
%\VignetteIndexEntry{Rle Tips and Tricks}
|
|
%\VignetteEngine{knitr::rmarkdown}
|
|
%\VignetteEncoding{UTF-8}
|
|
output:
|
|
BiocStyle::html_document
|
|
---
|
|
|
|
```{r Rle-rollmean, eval=FALSE}
|
|
rollmeanRle <- function (x, k)
|
|
{
|
|
n <- length(x)
|
|
cumsum(c(Rle(sum(window(x, 1, k))), window(x, k + 1, n) - window(x, 1, n - k))) / k
|
|
}
|
|
```
|
|
|
|
```{r Rle-rollvar, eval=FALSE}
|
|
rollvarRle <- function(x, k)
|
|
{
|
|
n <- length(x)
|
|
means <- rollmeanRle(x, k)
|
|
nextMean <- window(means, 2, n - k + 1)
|
|
cumsum(c(Rle(sum((window(x, 1, k) - means[1])^2)),
|
|
k * diff(means)^2 - (window(x, 1, n - k) - nextMean)^2 + (window(x, k + 1, n) - nextMean)^2)) / (k - 1)
|
|
}
|
|
```
|
|
|
|
```{r Rle-rollcov, eval=FALSE}
|
|
rollcovRle <- function(x, y, k)
|
|
{
|
|
n <- length(x)
|
|
meanX <- rollmeanRle(x, k)
|
|
meanY <- rollmeanRle(y, k)
|
|
nextMeanX <- window(meanX, 2, n - k + 1)
|
|
nextMeanY <- window(meanY, 2, n - k + 1)
|
|
cumsum(c(Rle(sum((window(x, 1, k) - meanX[1]) * (window(y, 1, k) - meanY[1]))),
|
|
k * diff(meanX) * diff(meanY) - (window(x, 1, n - k) - nextMeanX) * (window(y, 1, n - k) - nextMeanY) + (window(x, k + 1, n) - nextMeanX) * (window(y, k + 1, n) - nextMeanY))) / (k - 1)
|
|
}
|
|
```
|
|
|
|
```{r Rle-rollsd, eval=FALSE}
|
|
rollsdRle <- function(x, k)
|
|
{
|
|
sqrt(rollvarRle(x, k))
|
|
}
|
|
```
|
|
|
|
```{r Rle-rollcor,eval=FALSE}
|
|
rollcorRle <- function(x, y, k)
|
|
{
|
|
rollcovRle(x, y, k) / (rollsdRle(x, k) * rollsdRle(y, k))
|
|
}
|
|
```
|