makeOrderings {baySeq} | R Documentation

## Construct orderings for count data given a model structure and an ordering function.

### Description

Given a model structure as defined in the ‘@groups’ slot of a `countData` object containing more than one group, it is often possible to define an ordering on the groups for a given genomic event. To take a simple example, if the average expression of a gene is higher in sample set A then in sample set B, then we might impose an ordering A>B.

### Usage

    makeOrderings(cD, orderingFunction)

### Arguments

`cD` | A `countData` object, or a descendant thereof.
`orderingFunction` | A function defining the orderings. If not given, will be taken from the ‘@densityFunction’ slot of ‘cD’. See Details, and examples below.

### Details

The orderingFunction takes 'dat' and 'observables' as arguments. 'dat' is equivalent to the ‘@data’ slot of the ‘cD’ object, and 'observables' the combined data in the ‘@sampleObservables’, ‘@rowObservables’ and ‘@cellObservables’ slots.

### Value

A `countData` with populated ‘@orderings’ slot.

### Author(s)

Thomas J. Hardcastle

### References

Hardcastle T.J., and Kelly, K. baySeq: Empirical Bayesian Methods For Identifying Differential Expression In Sequence Count Data. BMC Bioinformatics (2010)

### Examples

    # load test data
    data(simData)

    # Create a countData object from test data

    replicates <- c("simA", "simA", "simA", "simA", "simA", "simB", "simB", "simB", "simB", "simB")
    groups <- list(NDE = c(1,1,1,1,1,1,1,1,1,1), DE = c(1,1,1,1,1,2,2,2,2,2))
    CD <- new("countData", data = simData, replicates = replicates, groups = groups)
    libsizes(CD) <- getLibsizes(CD)

    # order on expression normalised for library size (scaling factor) and gene length

    CD <- makeOrderings(CD, orderingFunction = function(dat, observables) dat / observables$libsizes)

    # orderings calculated for DE group
    head(CD@orderings)

    # load test (paired) data
    data(pairData)

    # create a countData object from paired data
    pairCD <- new("countData", data = list(pairData[,1:4], pairData[,5:8]),
                      replicates = c(1,1,2,2),
                      groups = list(NDE = c(1,1,1,1), DE = c(1,1,2,2)),
                   densityFunction = bbDensity)
    libsizes(pairCD) <- getLibsizes(pairCD)

    # order on (log-)ratio of pairs, with fudge-factor on zeros.

    pairCD <- makeOrderings(pairCD, orderingFunction = function(dat, observables) {
                                          data <- dat / observables$libsizes
                                          adjmin <- min(data[data > 0]) / 10
                                          log(data[,,1] + adjmin) - log(data[,,2] + adjmin)
    })

    # orderings calculated for DE group
    head(pairCD@orderings)

[Package baySeq version 2.24.0 Index]