alignPeaks {htSeqTools} | R Documentation

## Align peaks in a ChIP-Seq experiment by removing the strand specific bias.

### Description

Align peaks in a ChIP-Seq experiment by removing the shift between reads aligned to the plus and the minus strands.

### Usage

    alignPeaks(x, strand, npeaks = 1000, bandwidth = 150, mc.cores=1)

### Arguments

`x` | A `list`, `RangedData` or an `IRangesList` object containing the aligned reads in each chromosome.
`strand` | Strand that each read was aligned to. If `x` is of class `list`, `strand` can be a character vector of length 1 indicating the name of the field in `x` indicating the strand, i.e. `x[[1]][[strand]]` contains the strand information.
`npeaks` | Number of peaks to be used to estimate the shift size.
`bandwidth` | Only reads with distance less than `bandwidth` between them and their closest gene are used to estimate the shift size.
`mc.cores` | Number of cores to be used for parallel computing (passed on to `mclapply`). Only used if `x` is of class `list`.

### Details

The procedure detects the `npeaks` highest peaks (using reads from both strands simultaneously). Then it selects reads which are less than `bandwidth` base pairs away from any of the peaks. Then it computes (a) the average distance between reads on the plus strand and the closest peak, (b) the same distance for reads on the minus strand. The mean difference between (a) and (b) is the estimated shift size. Reads on the plus strand are shifted to the right, whereas reads on the minus strands are shifted to the left.

### Value

A `CompressedIRangesList` object with all reads shifted so that the strand specific bias is no longer present.

### Methods

`signature(x = "IRangesList", strand = "list")`

  Each element in `x` corresponds to a chromosome, and each range gives the start/end of a sequence. `strand` indicates the strand for the ranges in `x`.

`signature(x = "RangedData", strand = "character")`

  `x` gives read start and end positions, and `strand` gives the name of the variable in `values(x)` containing the strand information.

`signature(x = "list", strand = "character")`

  The method for `RangedData` is applied to each element in `x` separately, as each element may have a different strand-specific bias.

### Examples

    #Generate 1000 reads containing strand-specific bias
    st <- runif(1000,1,250)
    strand <- rep(c('+','-'),each=500)
    st[strand=='-'] <- st[strand=='-'] + runif(500,50,100)
    x <- RangedData(IRanges(st,st+38),strand=strand)
    #Estimate and remove the bias
    xalign <- alignPeaks(x, strand='strand', npeaks=1)

[Package htSeqTools version 1.30.0 Index]