fraction.target

<code><a rd-options="IRanges:RangedData-class" href="/link/RangedData?package=TEQC&version=3.12.0&to=IRanges%3ARangedData-class" data-mini-rdoc="IRanges:RangedData-class::RangedData">RangedData</a></code> table containing positions
      of target regions, i.e. output from <code><a rd-options="" href="/link/get.targets?package=TEQC&version=3.12.0" data-mini-rdoc="TEQC::get.targets">get.targets</a></code>

targets

integer; add <code>Offset</code> bases on both sides to targeted regions and potentially
      collapse resulting overlapping target regions

Offset

genome version targets were designed and reads aligned to.
      For the given options the total genome size is set automatically. For other genomes or versions,
      leave this option empty ('NA') and specify the genome size with option 'genomesize'

genome

integer: specify the total genome size manually. If 'genomesize' is given,
      option 'genome' will be ignored.

genomesize

Calculates the fraction of the reference genome that is targeted

 math

Target capture experiments combine hybridization-based (in
solution or on microarrays) capture and enrichment of genomic
regions of interest (e.g. the exome) with high throughput
sequencing of the captured DNA fragments. This package provides
functionalities for assessing and visualizing the quality of
the target enrichment process, like specificity and sensitivity
of the capture, per-target read coverage and so on.

Manuela Hummel

TEQC

Quality control for target capture experiments

fraction.target function

<code><a href="RangedData" rd-options="IRanges:RangedData-class">RangedData</a></code> table containing positions
      of target regions, i.e. output from <code><a href="get.targets" rd-options="">get.targets</a></code>

integer; add <code>Offset</code> bases on both sides to targeted regions and potentially
      collapse resulting overlapping target regions

genome version targets were designed and reads aligned to.
      For the given options the total genome size is set automatically. For other genomes or versions,
      leave this option empty ('NA') and specify the genome size with option 'genomesize'

integer: specify the total genome size manually. If 'genomesize' is given,
      option 'genome' will be ignored.

fraction.target: Fraction of the target within the genome

Description

Usage

Arguments

Value

See Also

Examples