RleDataFrame-views {genoset} | R Documentation

## Calculate summary statistics on views of an RleDataFrame

### 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

    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

    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)

[Package genoset version 1.38.0 Index]