normalizeCNV: Normalize CNV biases

In LTLA/diffHic: Differential Analysis of Hi-C Data

Normalize CNV biases

Description

Compute normalization offsets to remove CNV-driven and abundance-dependent biases

Usage

normalizeCNV(data, margins, prior.count=3, span=0.3, maxk=500, 
    assay.data=1, assay.marg=1, ...)

matchMargins(data, margins)

Arguments

data	an InteractionSet object produced by squareCounts
margins	a RangedSummarizedExperiment object produced by marginCounts
prior.count	a numeric scalar specifying the prior count to use in computing marginal log-ratios
span	a numeric scalar between 0 and 1, describing the span of the fit
maxk	a integer scalar specifying the number of vertices to use during local fitting
assay.data	a string or integer scalar specifying the matrix to use from data
assay.marg	a string or integer scalar specifying the matrix to use from margins
...	other arguments to pass to locfit

Details

Each bin pair in data is associated with three covariates. The first two are the marginal log-ratios of the corresponding bins, i.e., the log-ratio of the marginal counts between two libraries. These represent the relative CNVs in the interacting regions between libraries. To avoid redundancy, the first covariate is the larger marginal log-ratio whereas the second is the smaller. The third covariate is the average abundance across all libraries.

Each bin pair is also associated with a response, i.e., the log-ratio of the interaction counts between two libraries. A loess-like surface is fitted to the response against the three covariates, using the locfit function. The aim is to eliminate systematic differences between libraries at any combination of covariate values. This removes CNV-driven biases as well as trended biases with respect to the abundance. The fitted value can then be used as a GLM offset for each bin pair.

The objects in data and margins should be constructed with the same width and param arguments in their respective functions. This ensures that the regions are the same, so that the marginal counts can be directly used. Matching of the bins in each bin pair in data to indices of margins is performed using matchMargins. Note that the marginal counts are not directly computed from data as filtering of bin pairs may be performed beforehand.

In practice, normalization offsets are computed for each library relative to a single reference “average” library. This average library is constructed by using the average abundance as the (log-)count for both the bin pair and marginal counts. The space of all pairs of CNV log-ratios is also rotated by 45 degrees prior to smoothing. This improves the performance of the approximations used by locfit.

The fit parameters can be changed by varying span, maxk and additional arguments in locfit. Higher values of span will increase smoothness, at the cost of sensitivity. Increases in maxk may be required to obtain a more accurate approximation when fitting large datasets. In all cases, a loess fit of degree 1 is used.

For use by downstream functions, the offset matrix can be stored as an assay named "offset" in the data object.

Value

For normalizeCNV, a numeric matrix is returned with the same dimensions as counts(data). This contains log-based GLM offsets for each bin pair in each library.

For matchMargins, a data frame is returned with integer fields anchor1 and anchor2. Each field specifies the index in margins corresponding to the bin regions for each bin pair in data.

Author(s)

Aaron Lun

See Also

locfit, lp, squareCounts, marginCounts

Examples

# Dummying up some data.
set.seed(3423746)
npts <- 100
npairs <- 5000
nlibs <- 4
anchor1 <- sample(npts, npairs, replace=TRUE)
anchor2 <- sample(npts, npairs, replace=TRUE)

data <- InteractionSet(
    list(counts=matrix(rpois(npairs*nlibs, runif(npairs, 10, 100)), nrow=npairs)),
    GInteractions(anchor1=anchor1, anchor2=anchor2, 
        regions=GRanges("chrA", IRanges(1:npts, 1:npts)), mode="reverse"),
	colData=DataFrame(totals=runif(nlibs, 1e6, 2e6))) 

margins <- SummarizedExperiment(matrix(rpois(npts*nlibs, 100), nrow=npts),
	colData=DataFrame(totals=data$totals), rowRanges=regions(data))

# Running normalizeCNV.
out <- normalizeCNV(data, margins)
head(out)
head(normalizeCNV(data, margins, prior.count=1))
head(normalizeCNV(data, margins, span=0.5))

# Store offsets as the 'offset' assay for use by, e.g., asDGEList.
assays(data)$offset <- out
data

# Occasionally locfit will complain; increase maxk to compensate.
data <- InteractionSet(matrix(rpois(npairs*nlibs, 20), nrow=npairs),
    GInteractions(anchor1=anchor1, anchor2=anchor2,
        regions=GRanges("chrA", IRanges(1:npts, 1:npts)), mode="reverse"),
	colData=DataFrame(totals=runif(nlibs, 1e6, 2e6)))
tryCatch(head(normalizeCNV(data, margins, maxk=100)), error=function(e) e)
head(normalizeCNV(data, margins, maxk=1000))

# Matching margins.
matched <- matchMargins(data, margins)
head(matched)
anchor1.counts <- margins[matched$anchor1,]
anchor2.counts <- margins[matched$anchor2,]

LTLA/diffHic documentation built on Dec. 20, 2024, 7:06 p.m.