twilight.filtering {twilight} | R Documentation

## Permutation filtering

### Description

The function call invokes the filtering for permutations of class labels that produce a set of complete null scores. Depending on the test setting, the algorithm iteratively generates valid permutations of the class labels and computes scores. These are transformed to pooled p-values and each set of permutation p-values is tested for uniformity. Permutations with acceptable uniform p-value distributions are kept. The search stops if either the number `num.perm` of wanted permutations is reached or if the number of possible unique(!) permutations is smaller than `num.perm`. The default values are similar to function `twilight.pval` but please note the details below.

### Usage

    twilight.filtering(xin, yin, method = "fc", paired = FALSE, s0 = 0, verbose = TRUE, num.perm = 1000, num.take = 50)

### Arguments

`xin` | Either an expression set (`ExpressionSet`) or a data matrix with rows corresponding to features and columns corresponding to samples.
`yin` | A numerical vector containing class labels. The higher label denotes the case, the lower label the control samples to test case vs. control. For correlation scores, `yin` can be any numerical vector of length equal to the number of samples.
`method` | Character string: `"fc"` for fold change equivalent test (that is log ratio test), `"t"` for t-test, and `"z"` for Z-test. With `"pearson"` or `"spearman"`, the test statistic is either Pearson's correlation coefficient or Spearman's rank correlation coefficient.
`paired` | Logical value. Depends on whether the samples are paired. Ignored if `method="pearson"` or `method="spearman"`.
`s0` | Fudge factor for variance correction in the Z-test. Takes effect only if `method="z"`. If `s0=0`: The fudge factor is set to the median of the pooled standard deviations.
`verbose` | Logical value for message printing.
`num.perm` | Number of permutations. Within `twilight.pval`, `num.perm` is set to `B`.
`num.take` | Number of permutations kept in each step of the iterative filtering. Within `twilight.pval`, `num.take` is set to the minimum of 50 and `ceiling(num.perm/20)`.

### Details

See vignette.

### Value

Returns a matrix with permuted input labels `yin` as rows. Please note that this matrix is already translated into binary labels for two-sample testing or to ranks if Spearman's correlation was chosen. The resulting permutation matrix can be directly passed into function `twilight.pval`. Please note that the first row always contains the original input `yin` to be consistent with the other permutation functions in package `twilight`.

### Author(s)

Stefanie Scheid http://www.molgen.mpg.de/~scheid

### References

Scheid S and Spang R (2004): A stochastic downhill search algorithm for estimating the local false discovery rate, IEEE TCBB 1(3), 98–108.

Scheid S and Spang R (2005): twilight; a Bioconductor package for estimating the local false discovery rate, Bioinformatics 21(12), 2921–2922.

Scheid S and Spang R (2006): Permutation filtering: A novel concept for significance analysis of large-scale genomic data, in: Apostolico A, Guerra C, Istrail S, Pevzner P, and Waterman M (Eds.): Research in Computational Molecular Biology: 10th Annual International Conference, Proceedings of RECOMB 2006, Venice, Italy, April 2-5, 2006. Lecture Notes in Computer Science vol. 3909, Springer, Heidelberg, pp. 338-347.

### See Also

`twilight.pval`

### Examples

    ## Not run:
    ### Leukemia data set of Golub et al. (1999).
    library(golubEsets)
    data(Golub_Train)

    ### Variance-stabilizing normalization of Huber et al. (2002).
    library(vsn)
    golubNorm <- justvsn(Golub_Train)

    ### A binary vector of class labels.
    id <- as.numeric(Golub_Train$ALL.AML)

    ### Do an unpaired t-test.
    ### Let's have a quick example with 50 filtered permutations only.
    ### With num.take=10, we only need 5 iteration steps.
    yperm <- twilight.filtering(golubNorm,id,method="t",num.perm=50,num.take=10)
    dim(yperm)

    ### Let's check that the filtered permutations really produce uniform p-value distributions.
    ### The first row is the original labeling, so we try the second permutation.
    yperm <- yperm[-1,]
    b <- twilight.pval(golubNorm,yperm[1,],method="t",yperm=yperm)
    hist(b$result$pvalue)

    ## End(Not run)

[Package twilight version 1.60.0 Index]