coerce-functions: Create SummarizedExperiment representations by transforming...

Description Usage Arguments Value Examples

Description

These methods transform RaggedExperiment objects to similar SummarizedExperiment objects. They do so by transforming assay data to more rectangular representations, following the rules outlined for similarly names transformations sparseAssay(), compactAssay(), disjoinAssay(), and qreduceAssay(). Because of the complexity of the transformation, ti usually only makes sense transform RaggedExperiment objects with a single assay; this is currently enforced at time of coercion.

Usage

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sparseSummarizedExperiment(x, i = 1, withDimnames = TRUE)

compactSummarizedExperiment(x, i = 1L, withDimnames = TRUE)

disjoinSummarizedExperiment(x, simplify, i = 1L, withDimnames = TRUE)

qreduceSummarizedExperiment(x, query, simplify, i = 1L, withDimnames = TRUE)

Arguments

x

RaggedExperiment

i

integer(1), character(1), or logical() selecting the assay to be transformed.

withDimnames

logical(1) default TRUE. propagate dimnames to SummarizedExperiment.

simplify

function of 1 (for disjoinSummarizedExperiment) or 3 (for qreduceSummarizedExperiment) arguments, used to transform assays. See assay-functions.

query

GRanges provding regions over which reduction is to occur.

Value

All functions return RangedSummarizedExperiment.

sparseSummarizedExperiment has rowRanges() identical to the row ranges of x, and assay() data as sparseAssay(). This is very space-inefficient representation of ragged data.

compactSummarizedExperiment has rowRanges() identical to the row ranges of x, and assay() data as compactAssay(). This is space-inefficient representation of ragged data when samples are primarily composed of different ranges.

disjoinSummarizedExperiment has rowRanges() identical to the disjoint row ranges of x, disjoint(rowRanges(x)), and assay() data as disjoinAssay().

qreduceSummarizedExperiment has rowRanges() identical to query, and assay() data as qreduceAssay().

Examples

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x <- RaggedExperiment(GRangesList(
    GRanges(c("A:1-5", "A:4-6", "A:10-15"), score=1:3),
    GRanges(c("A:1-5", "B:1-3"), score=4:5)
))

## sparseSummarizedExperiment

sse <- sparseSummarizedExperiment(x)
assay(sse)
rowRanges(sse)

## compactSummarizedExperiment

cse <- compactSummarizedExperiment(x)
assay(cse)
rowRanges(cse)

## disjoinSummarizedExperiment

disjoinAssay(x, lengths)
dse <- disjoinSummarizedExperiment(x, lengths)
assay(dse)
rowRanges(dse)

## qreduceSummarizedExperiment

x <- RaggedExperiment(GRangesList(
    GRanges(c("A:1-3", "A:4-5", "A:10-15"), score=1:3),
    GRanges(c("A:4-5", "B:1-3"), score=4:5)
))
query <- GRanges(c("A:1-2", "A:4-5", "B:1-5"))

weightedmean <- function(scores, ranges, qranges)
    ## weighted average score per query range
    sum(scores * width(ranges)) / sum(width(ranges))

qreduceAssay(x, query, weightedmean)
qse <- qreduceSummarizedExperiment(x, query, weightedmean)
assay(qse)
rowRanges(qse)

Bioconductor-mirror/RaggedExperiment documentation built on Aug. 10, 2017, 10:44 a.m.