# RleDataFrame-views: Calculate summary statistics on views of an RleDataFrame In genoset: A RangedSummarizedExperiment with methods for copy number analysis

## Description

These methods mirror the viewMeans type functions from IRanges for SimpleRleList. They differ in that they work on an RleDataFrame and an IRanges directly and also have a simplify argument. This works out to be faster (compute-wise) and also convenient.

Still, an RleDataFrame inherits from SimpleRleList, so all of the views functions will work.

## Usage

 ```1 2 3 4 5 6``` ```rangeSums(x, bounds, na.rm=FALSE, simplify=TRUE) rangeMeans(x, bounds, na.rm=FALSE, simplify=TRUE, ...) rangeMins(x, bounds, na.rm=FALSE, simplify=TRUE) rangeMaxs(x, bounds, na.rm=FALSE, simplify=TRUE) rangeWhichMins(x, bounds, na.rm=FALSE, simplify=TRUE) rangeWhichMaxs(x, bounds, na.rm=FALSE, simplify=TRUE) ```

## Arguments

 `x` RleDataFrame `bounds` Matrix with two columns or IRanges representing ranges of rows of `x` to process. If `bounds` is a matrix, an IRanges is constructed assuming the first two columns represent the start and end of the ranges. The names for the IRanges is taken from the rownames of the matrix. Such a matrix can constructed with `boundingIndicesByChr` and is the preferred input. `na.rm` Scalar logical. Ignore NAs in calculations? `simplify` Scalar logical. Simplify result? If TRUE, the return value will be a vector or matrix. For a single view, a vector will be returned. Otherwise a matrix with one row per view and one column per column of x will be returned. If FALSE, the return value will be a list of length `ncol(x)` of vectors of length `nrow(bounds)`. `...` Additional arguments for other methods.

## Details

The "range" name prefixes here serve to differentiate these functions from the "view" functions. This may change. I will be asking the IRanges team to add "..." and "simplify" to the "view" methods so that I can just make additional methods for `RleDataFrame`.

## Value

With `simplify == TRUE`, a vector for single view or a matrix otherwise. When `simplify == FALSE`, a list of vectors length ncol(x) where each element is of length `nrows(bounds)`.

## See Also

RleDataFrame boundingIndicesByChr

## Examples

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19``` ```df = RleDataFrame(list(a=Rle(1:5, rep(2, 5))), b=Rle(1:5, rep(2, 5)), row.names=LETTERS[1:10]) mat = matrix(c(1,4,3,5),ncol=2,dimnames=list(c("Gene1","Gene2"),c("start","end"))) bounds = IRanges(start=c(1, 4), end=c(3, 5), names=c("Gene1","Gene2")) rangeMeans(df,bounds,simplify=FALSE) rangeMeans(df,bounds,simplify=TRUE) rangeMeans(df,mat,simplify=TRUE) rangeMeans(df,bounds) rangeSums(df,bounds) rangeMins(df,bounds) rangeMaxs(df,bounds) rangeWhichMins(df,bounds) rangeWhichMaxs(df,bounds) # RleDataFrame isa SimpleRleList, so all the IRanges view* methods work too: v = RleViewsList( lapply( df, Views, start=bounds ) ) viewMeans(v) ```

genoset documentation built on Nov. 8, 2020, 6:07 p.m.