filterDuplReads {htSeqTools} | R Documentation

## Detect and filter duplicated reads/sequences.

### Description

`filterDuplReads` filters highly repeated sequences, i.e. with the same chromosome, start and end positions. As many such sequences are likely due to over-amplification artifacts, this can be a useful pre-processing step for ultra high-throughput sequencing data. A false discovery rate is computed for each number of repeats being unusually high. The reads with a higher false discovery rate will be removed. For more information on the false discovery rate calculation please read the `fdrEnrichment` manual.

`tabDuplReads` counts the number reads with no duplications, duplicated once, twice etc.

### Usage

    filterDuplReads(x, maxRepeats, fdrOverAmp=0.01, negBinomUse=.999,components=0, mc.cores=1)

    tabDuplReads(x,  minRepeats=1, mc.cores=1)

### Arguments

`x` | Object containing read locations. Currently methods for `RangedData` and `list`. Duplication is assessed based only on the space, start, end and `x[['strand']]`, i.e. even if they are different based on other variables stored in `values(x)`, the reads are considered duplicated and only the first appearance is returned.
`maxRepeats` | Reads appearing `maxRepeats` or more times will be excluded. If not specified, this is setup automatically based on `fdrOverAmp`.
`fdrOverAmp` | Reads with false discovery rate of being over-amplified greater than `fdrOverAmp` are excluded.
`negBinomUse` | Number of counts that will be used to compute the null distribution. Using 1 - 1/1000 would mean that 99.9% of the reads will be used. The ones with higher number of repetitions are the excluded ones.
`components` | number of negative binomials that will be used to fit null distribution. The default value is 1. This value hase to be between 0 and 4. If 0 is given the optimal number of negative biomials is choosen using the Bayesian information criterion (BIC)
`mc.cores` | Number of cores to be used in parallel computing (passed on to `mclapply`).
`minRepeats` | The table is only produced for reads with at least `minRepeats` repeats.

### Value

`filterDuplReads` returns `x` without highly repetitive sequencesas, determined by `maxRepeats` or `ppOverAmp`.

`tabDuplReads` returns a table counting the number of sequences repeating 1 times, 2 times, 3 times etc.

### Methods

Methods for `filterDuplReads` and `tabDuplReads`

`signature(x = "RangedData")`

  Two reads are duplicated if they have the same space, start and end position.

`signature(x = "list")`

  The method is applied separately to each `RangedData` element in the list.

### Author(s)

Evarist Planet, David Rossell, Oscar Flores

### See Also

`fdrEnrichedCounts` to compute the posterior probability that a certain number of repeats is due to over-amplification.

### Examples

    set.seed(1)
    st <- round(rnorm(1000,500,100))
    strand <- rep(c('+','-'),each=500)
    space <- sample(c('chr1','chr2'),size=length(st),replace=TRUE)
    sample1 <- RangedData(IRanges(st,st+38),strand=strand,space=space)

    #Add artificial repeats
    st <- rep(400,20)
    repeats <- RangedData(IRanges(st,st+38),strand='+',space='chr1')
    sample1 <- rbind(sample1,repeats)

    filterDuplReads(sample1)

[Package htSeqTools version 1.28.3 Index]