zScore {sparrow} | R Documentation

## Calculate single sample geneset score by average z-score method

### Description

Calculate single sample geneset score by average z-score method

### Usage

    zScore(x, summary = c("mean", "sqrt"), trim = 0, ...)

### Arguments

`x` | gene x sample matrix with rows already subsetted to the ones you care about.
`summary` | sqrt or mean
`trim` | calculate trimmed mean?
`...` | pass through arguments

### Value

A list of stats related to the zscore. You care mostly about `$score`.

### Examples

    vm <- exampleExpressionSet(do.voom=TRUE)
    gdb <- conform(exampleGeneSetDb(), vm)
    features <- featureIds(gdb, 'c2', 'BURTON_ADIPOGENESIS_PEAK_AT_2HR',
                           value='x.idx')
    zscores <- zScore(vm[features,])

    ## Use scoreSingleSamples to facilitate scoring of all gene sets
    scores.all <- scoreSingleSamples(gdb, vm, 'zscore', summary = "mean")
    s2 <- with(subset(scores.all, name == 'BURTON_ADIPOGENESIS_PEAK_AT_2HR'),
               setNames(score, sample_id))
    all.equal(s2, zscores$score)

[Package sparrow version 1.0.3 Index]