fragmentLenDetect {nucleR} | R Documentation

## Fragments length detection from single-end sequencing samples

### Description

When using single-ended sequencing, the resulting partial sequences map only in one strand, causing a bias in the coverage profile if not corrected. The only way to correct this is knowing the average size of the real fragments. `nucleR` uses this information when preprocessing single-ended sequences. You can provide this information by your own (usually a 147bp length is a good aproximation) or you can use this method to automatically guess the size of the inserts.

### Usage

    fragmentLenDetect(reads, samples = 1000, window = 5000, min.shift = 1,
      max.shift = 100, mc.cores = 1, as.shift = FALSE)

    ## S4 method for signature 'AlignedRead'
    fragmentLenDetect(reads, samples = 1000,
      window = 1000, min.shift = 1, max.shift = 100, mc.cores = 1,
      as.shift = FALSE)

    ## S4 method for signature 'GRanges'
    fragmentLenDetect(reads, samples = 1000, window = 1000,
      min.shift = 1, max.shift = 100, mc.cores = 1, as.shift = FALSE)

    ## S4 method for signature 'RangedData'
    fragmentLenDetect(reads, samples = 1000,
      window = 1000, min.shift = 1, max.shift = 100, mc.cores = 1,
      as.shift = FALSE)

### Arguments

`reads` | Raw single-end reads ShortRead::AlignedRead or GenomicRanges::GRanges format)
`samples` | Number of samples to perform the analysis (more = slower but more accurate)
`window` | Analysis window. Usually there's no need to touch this parameter.
`min.shift, max.shift` | Minimum and maximum shift to apply on the strands to detect the optimal fragment size. If the range is too big, the performance decreases.
`mc.cores` | If multicore support, maximum number of cores allowed to use.
`as.shift` | If TRUE, returns the shift needed to align the middle of the reads in opposite strand. If FALSE, returns the mean inferred fragment length.

### Details

This function shifts one strand downstream one base by one from `min.shift` to `max.shift`. In every step, the correlation on a random position of length `window` is checked between both strands. The maximum correlation is returned and averaged for `samples` repetitions.

The final returned length is the best shift detected plus the width of the reads. You can increase the performance of this function by reducing the `samples` value and/or narrowing the shift range. The `window` size has almost no impact on the performance, despite a to small value can give biased results.

### Value

Inferred mean lenght of the inserts by default, or shift needed to align strands if `as.shift=TRUE`.

### Author(s)

Oscar Flores oflores@mmb.pcb.ub.es

### Examples

    library(GenomicRanges)
    library(IRanges)

    # Create a sinthetic dataset, simulating single-end reads, for positive and
    # negative strands
    # Positive strand reads
    pos <- syntheticNucMap(nuc.len=40, lin.len=130)$syn.reads
    # Negative strand (shifted 147bp)
    neg <- IRanges(end=start(pos)+147, width=40)
    sim <- GRanges(
        seqnames="chr1",
        ranges=c(pos, neg),
        strand=c(rep("+", length(pos)), rep("-", length(neg)))
    )

    # Detect fragment lenght (we know by construction it is really 147)
    fragmentLenDetect(sim, samples=50)
    # The function restricts the sampling to speed up the example

[Package nucleR version 2.14.0 Index]