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