pvalRRHO: Compute the significance of the overlap between two lists

Description Usage Arguments Details Value Note Author(s) See Also Examples

View source: R/ExpressionAnalysis.R

Description

Computes the significance of the agreements between lists as returned by RRHO using resampling.

Usage

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pvalRRHO(RRHO.obj, replications, stepsize=RRHO.obj$stepsize, FUN= max)

Arguments

RRHO.obj

The output object of the RRHO function.

replications

The number of samples to be taken from the distribution of the aggregated test statistic.

stepsize

Controls the resolution of the test: how many items between any two overlap tests (i.e., netween any two i-s and two j-s.)

FUN

The function aggregating infomation from the whole overlap matrix into one summary statistic. Typically the min pvalue, or max on -log(pval) scale.

Details

The distribution of FUN(-log(pval)) is computed using resampling.

The aggregating function will typically be the max function, corresponding to the maximal -log(pvalue), i.e., the most significant agreement over all sublists.

The distribution is computed by resampling pairs of null sequences, computing the significances of all the overlaps as done in the reference, applying the aggregating function supplied by the user, and returning the permutation based significance.

Value

pval

The FWER corrected significance of observed aggregated pvalue.

FUN.ecdf

The simulated sampling distribution of the aggregated pvalues.

FUN

The matrix aggregation function used. typicall max for minimal p-value.

n.items

Length of lists.

stepsize

See RRHO

replications

The number of simulation replications.

call

The function call.

Note

Might take a long time to run. Depending on the number of replications, the item (gene) count and the stepsize.

Also note that the significance returned is a conservative value (by a constant of 1/replications).

Author(s)

Jonathan Rosenblatt

See Also

RRHO

Examples

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list.length <- 100
list.names <- paste('Gene',1:list.length, sep='')
gene.list1<- data.frame(list.names, sample(list.length))
gene.list2<- data.frame(list.names, sample(list.length))
RRHO.example <-  RRHO(gene.list1, gene.list2, alternative='enrichment')
pval.testing <- pvalRRHO(RRHO.example,50) 

Example output

Loading required package: grid

RRHO documentation built on April 29, 2020, 5:20 a.m.