BindScore-class {ChIPseqR} | R Documentation

## Class "BindScore"

### Description

This class provides the infrastructure to store results of ChIP-seq analysis.

### Usage

    	## S4 method for signature 'BindScore'
    binding(x)
    	## S4 method for signature 'BindScore'
    chrLength(x, subset)
    	## S4 method for signature 'BindScore'
    cutoff(x, type=c("score", "pvalue"))
    	## S4 replacement method for signature 'BindScore'
    cutoff(x, type=c("score", "pvalue")) <- value
    	## S4 method for signature 'BindScore'
    head(x, n=6, by=c("score", "position"), ...)
    	## S4 method for signature 'BindScore'
    lapply(X, FUN, ...)
    	## S4 method for signature 'BindScore'
    length(x)
    	## S4 replacement method for signature 'BindScore'
    length(x) <- value
    	## S4 method for signature 'BindScore'
    max(x, ..., na.rm=TRUE)
    	## S4 method for signature 'BindScore'
    min(x, ..., na.rm=TRUE)
    	## S4 method for signature 'BindScore'
    names(x)
    	## S4 replacement method for signature 'BindScore,ANY'
    names(x) <- value
    	## S4 method for signature 'BindScore'
    nullDist(x)
    	## S4 replacement method for signature 'BindScore'
    nullDist(x) <- value
    	## S4 method for signature 'BindScore'
    peaks(x, ...)
    	## S4 method for signature 'BindScore'
    range(x, ..., na.rm=TRUE)
    	## S4 method for signature 'BindScore'
    score(x)
    	## S4 method for signature 'BindScore'
    support(x)
    	## S4 method for signature 'BindScore'
    tail(x, n=6, by=c("score", "position"), ...)
    	BindScore(call, score=list(), pvalue=list(), peaks=list(), cutoff=c(-Inf, 1), nullDist=c(0, 1), names=NULL, start=1L, compress=TRUE, digits=16)

### Arguments

`x` | Object of class `BindScore`.
`X` | Object of class `BindScore`.
`subset` | Index vector indicating a subset of `x`. If `subset` is missing everything is selected.
`type` | A string indicating which type of cut-off should be returned or changed. Either `"score"` or `"pvalue"`
`n` | Number of entries to show.
`by` | A string indicating whether the output should be sorted by score or by position in the genome.
`na.rm` | Logical indication whether `NA`s should be ignored.
`FUN` | Function to apply to results for each chromosome.
`value` | Replacement value.
`call` | Function call used to generate the values of the other slots.
`score` | List of binding site scores. One component per chromosome.
`pvalue` | List of binding site p-values. One component per chromosome.
`peaks` | List of significant peaks in binding site score. One component per chromosome.
`cutoff` | Numeric vector of length two indicating the significance cut-off in terms of score and p-value.
`nullDist` | Parameters of the null distribution.
`names` | Character vector providing names for chromosomes.
`start` | Integer indicating position of first binding site score.
`compress` | Logical indicating whether scores and p-values should be compressed.
`digits` | The number of decimal places to retain for compression.
`...` | Further arguments.

### Objects from the Class

Objects can be created by calls of the form `new("BindScore", functionCall, score, pvalue, peaks, cutoff, nullDist, names, ...)`. Objects of this class are typically created (and returned) by functions that perform peak calling on ChIP-seq data. Usually there should be no need to create them directly.

### Slots

`functionCall`:

  Object of class `"call"` storing the function call used to initiate the analysis.

`score`:

  Object of class `"list"`. The binding site score. One numeric vector per chromosome.

`pvalue`:

  Object of class `"list"`. The (adjusted) p-values corresponding to the scores in slot `score`.

`peaks`:

  Object of class `"list"` giving the location of significant peaks in the binding site score. These correspond to the location of predicted binding sites.

`cutoff`:

  Object of class `"numeric"` with entries ‘pvalue’ and ‘score’ giving the significance threshold used for peak calling in terms of p-value and score.

`nullDist`:

  Object of class `"numeric"` providing the parameters of the null distribution used to determine p-values.

`start`:

  Object of class `"integer"` indicating the index corresponding to the first entry in `score` (assumed to be the same for all chromosomes).

### Methods

as.data.frame

  `signature(x = "BindScore")`: Convert results into a `data.frame` giving the location, score and p-value of significant peaks.

[

  `signature(x = "BindScore", i = "ANY", j = "missing", drop = "missing")`: Restrict results to a subset of chromosomes. Chromosomes can either be identified by name or by numerical index.

[[

  `signature(x = "BindScore", i = "ANY", j = "missing")`: Restrict results to a single chromosome. Note that `x[["chr1"]]` is identical to `x["chr1"]`.

[[

  `signature(x = "BindScore", i = "ANY", j = "numeric")`: subset results to restrict them to a region on a single chromosome.

binding

  `signature(x = "BindScore")`: Returns length of binding site used during analysis.

chrLength

  `signature(x = "BindScore", subset = "ANY")`: Returns length of all chromosomes represented in `x`.

cutoff<-

  `signature(x = "BindScore")`: Sets the significance cut-off. Argument `type=c("score", "pvalue")` determines which cut-off is to be set, the other is adjusted accordingly. This recalculates the significance of peaks in the binding site score and may be slow.

cutoff

  `signature(x = "BindScore")`: Returns significance threshold used for analysis.

head

  `signature(x = "BindScore")`: Returns the first `n` peaks. Argument `by = c("score", "position")` determines whether results are sorted by score or by genomic location.

lapply

  `signature(X = "BindScore")`: Applies a function to results for each chromosome.

length<-

  `signature(x = "BindScore")`: Reduces the number of chromosomes for which results are stored, i.e., `length(x) <- 3` only retains the first three chromosomes.

length

  `signature(x = "BindScore")`: Returns the number of binding sites identified by the analysis.

max

  `signature(x = "BindScore")`: Returns maximum score.

min

  `signature(x = "BindScore")`: Returns minimum score.

names<-

  `signature(x = "BindScore", value = "ANY")`: Sets the chromosome names.

names

  `signature(x = "BindScore")`: Returns the chromosome names.

nullDist<-

  `signature(x = "BindScore")`: Sets the parameters of the null distribution adjusting the significance cut-off in the process and predicts binding sites using the new null distribution.

peaks

  `signature(x = "BindScore")`: Returns list of predicted binding sites.

range

  `signature(x = "BindScore")`: Range of binding site scores.

score

  `signature(x = "BindScore")`: Returns list of binding site scores.

support

  `signature(x = "BindScore")`: Returns length of support region used during analysis.

tail

  `signature(x = "BindScore")`: Returns the last `n` peaks. Argument `by = c("score", "position")` determines whether results are sorted by score or by genomic location.

### Author(s)

Peter Humburg

### References

~put references to the literature/web site here ~

### See Also

`ReadCounts` for the data structure used as input for the analysis and `callBindingSites`

### Examples

    showClass("BindScore")

    set.seed(1)

    ## determine binding site locations
    b <- sample(1:1e6, 5000)

    ## sample read locations
    fwd <- unlist(lapply(b, function(x) sample((x-83):(x-73), 20, replace=TRUE)))
    rev <- unlist(lapply(b, function(x) sample((x+73):(x+83), 20, replace=TRUE)))

    ## add some background noise
    fwd <- c(fwd, sample(1:(1e6-25), 50000))
    rev <- c(rev, sample(25:1e6, 50000))

    ## create data.frame with read positions as input to strandPileup
    reads <- data.frame(chromosome="chr1", position=c(fwd, rev),
    	length=25, strand=factor(rep(c("+", "-"), times=c(150000, 150000))))

    ## create object of class ReadCounts
    readPile <- strandPileup(reads, chrLen=1e6, extend=1, plot=FALSE)

    ## predict binding site locations
    ## the artificial dataset is very small so predictions may not be very reliable
    bindScore <- simpleNucCall(readPile, bind=147, support=20, plot=FALSE, compress=FALSE)

    ## number of binding sites found
    length(bindScore)

    ## the first few predictions, by score
    head(bindScore)

    ## score and p-value cut-off used
    cutoff(bindScore)

[Package ChIPseqR version 1.48.0 Index]