swish {fishpond} | R Documentation

## swish: SAMseq With Inferential Samples Helps

### Description

Performs non-parametric inference on rows of `y` for various experimental designs. See References for details.

### Usage

    swish(
      y,
      x,
      cov = NULL,
      pair = NULL,
      interaction = FALSE,
      nperms = 100,
      estPi0 = FALSE,
      qvaluePkg = "qvalue",
      pc = 5,
      nRandomPairs = 30,
      fast = 1,
      returnNulls = FALSE,
      quiet = FALSE
    )

### Arguments

`y` | a SummarizedExperiment containing the inferential replicate matrices of median-ratio-scaled TPM as assays 'infRep1', 'infRep2', etc.
`x` | the name of the condition variable. A factor with two levels for a two group analysis (possible to adjust for covariate or matched samples, see next two arguments)
`cov` | the name of the covariate for adjustment. If provided a stratified Wilcoxon in performed. Cannot be used with `pair`
`pair` | the name of the pair variable, which should be the number of the pair. Can be an integer or factor. If specified, a signed rank test is used to build the statistic. All samples across `x` must be pairs if this is specified. Cannot be used with `cov`.
`interaction` | logical, whether to perform a test of an interaction between `x` and `cov`. See Details.
`nperms` | the number of permutations. if set above the possible number of permutations, the function will print a message that the value is set to the maximum number of permutations possible
`estPi0` | logical, whether to estimate pi0
`qvaluePkg` | character, which package to use for q-value estimation, `samr` or `qvalue`
`pc` | pseudocount for finite estimation of `log2FC`, not used in calculation of test statistics, `locfdr` or `qvalue`
`nRandomPairs` | the number of random pseudo-pairs (only used with `interaction=TRUE` and un-matched samples) to use to calculate the test statistic
`fast` | an integer, toggles different methods based on speed (`fast=1` is default, `0` is slower). See Details.
`returnNulls` | logical, only return the `stat` vector, the `log2FC` vector, and the `nulls` matrix (default FALSE)
`quiet` | display no messages

### Details

interaction: The interaction tests are different than the other tests produced by `swish`, in that they focus on a difference in the log2 fold change across levels of `x` when comparing the two levels in `cov`. If `pair` is specified, this will perform a Wilcoxon rank sum test on the two groups of matched sample LFCs. If `pair` is not included, multiple random pairs of samples within the two groups are chosen, and again a Wilcoxon rank sum test compared the LFCs across groups.

fast: '0' involves recomputing ranks of the inferential replicates for each permutation, '1' (default) is roughly 10x faster by avoiding re-computing ranks for each permutation. The `fast` argument is only relevant for the following three experimental designs: (1) two group Wilcoxon, (2) stratified Wilcoxon, e.g. `cov` is specified, and (3) the paired interaction test, e.g. `pair` and `cov` are specified. For paired design and general interaction test, there are not fast/slow alternatives.

### Value

a SummarizedExperiment with metadata columns added: the statistic (either a centered Wilcoxon Mann-Whitney or a signed rank statistic, aggregated over inferential replicates), a log2 fold change (the median over inferential replicates, and averaged over pairs or groups (if groups, weighted by sample size), the local FDR and q-value, as estimated by the `samr` package.

### References

The citation for `swish` method is:

Anqi Zhu, Avi Srivastava, Joseph G Ibrahim, Rob Patro, Michael I Love "Nonparametric expression analysis using inferential replicate counts" Nucleic Acids Research (2019). https://doi.org/10.1093/nar/gkz622

The `swish` method builds upon the `SAMseq` method, and extends it by incorporating inferential uncertainty, as well as providing methods for additional experimental designs (see vignette).

For reference, the publication describing the `SAMseq` method is:

Jun Li and Robert Tibshirani "Finding consistent patterns: A nonparametric approach for identifying differential expression in RNA-Seq data" Stat Methods Med Res (2013). https://doi.org/10.1177/0962280211428386

### Examples

    library(SummarizedExperiment)
    set.seed(1)
    y <- makeSimSwishData()
    y <- scaleInfReps(y)
    y <- labelKeep(y)
    y <- swish(y, x="condition")

    # histogram of the swish statistics
    hist(mcols(y)$stat, breaks=40, col="grey")
    cols = rep(c("blue","purple","red"),each=2)
    for (i in 1:6) {
      arrows(mcols(y)$stat[i], 20,
             mcols(y)$stat[i], 10,
             col=cols[i], length=.1, lwd=2)
    }

    # plot inferential replicates
    plotInfReps(y, 1, "condition")
    plotInfReps(y, 3, "condition")
    plotInfReps(y, 5, "condition")

[Package fishpond version 1.8.0 Index]