listOverlap {htSeqTools} | R Documentation

## Assess the overlap between two or three lists.

### Description

Assess the overlap between two or three lists, e.g. ChIP-Seq peaks vs. genes selected from a microarray, or peaks obtained in different experiments.

### Usage

    listOverlap(list1, list2, list3, univ, ...)

### Arguments

`list1` | Vector with elements in the first list. This can either be a character vector indicating the element names, or a named factor vector indicating some classification for the elements in the first list.
`list2` | Vector with elements in the second list. This should be a character vector indicating the element names.
`list3` | Vector with elements in the third list. This should be a character vector indicating the element names. The overlap assesment method used depends on whether this argument is specified or not. See details.
`univ` | character vector indicating the universe of all elements from which `list1` and `list2` were obtained. The overlap assessment depends on whether this argument is specified or not. See details.
`...` | Further arguments to be passed on to `chisq.test` in 2 list overlapping.

### Details

For signature(list1='character', list2='character', list3='missing', univ='character') the overlap is assessed with respect to the universe of all possible elements `univ`. That is, we count the number of elements that are common to list1 and list2, those appearing only in either list1 or list2, and those not appearing in either (but appearing in `univ`). A typical example: `list1` contains names of genes with a peak in ChIP-Seq experiment 1, `list2` names of genes with a peak in ChIP-Seq experiment 2, and `univ` the names of all genes in the organism.

For signature(list1='character', list2='character', list='character', univ='character') the overlap is assessed by fitting and anova comparison of linear models. This is done to test whether 3-way overlap is significant with respect to the universe of all possible elements `univ` when compared to a model considering just the combination of 2-way overlapping. A typical example: `list1`, `list2` and `list3` contain names of genes with peaks in three different ChIP-Seq experiments, and `univ` the names of all genes in the organism.

For signature(list1='factor', list2='character', univ='missing') the distribution of `list1` is compared between elements appearing and not appearing in `list2`. A typical example: `list1` indicates the differential expression status for a number of genes, and `list2` contains the names of the genes which had a peak in a ChIP-Seq experiment.

### Value

For comparison of 2 lists, an `htest` object from a chi-square test that evaluates if the two lists are statistically independent from each other. This is a named list: the observed overlap is stored in `observed` and the P-value in `p.value`.

For 3 list comparison, a `list` object containing the occurrence and frequency tables (`xtab`, `ftable`), the fitted linear models (`glm1`, `glm2`), and the anova P-value (`pvalue`).

### Methods

`signature(list1 = "character", list2 = "character", list3 = "character", univ = "character")`

  Studies 3-way associations.

`signature(list1 = "character", list2 = "character", list3 = "missing", univ = "character")`

  Studies bivariate associations.

`signature(list1 = "factor", list2 = "character", list3 = "missing", univ = "missing")`

  Studies bivariate associations.

### Examples

    #Overlap between diff expression and chip-seq peaks
    deStatus <- factor(c(0,0,0,0,1,1,1))
    names(deStatus) <- paste('Gene',1:7)
    peaks <- c('Gene 6','Gene 7')
    ans <- listOverlap(list1=deStatus,list2=peaks)
    ans$observed
    ans$p.value

    #Overlap between peaks obtained from two different experiments
    peaks2 <- c('Gene 1','Gene 2','Gene 7')
    univ <- paste('Gene',1:7)
    ans <- listOverlap(list1=peaks,list2=peaks2,univ=univ)
    ans$observed
    ans$p.value

[Package htSeqTools version 1.28.3 Index]