getFeatureCounts

<code>AlignedGenomeIntervals</code> object

<code>Genome\_intervals</code> objects of genomic features

character indicating which column of the object
    <code>FG</code> holds the identifiers of the genomic features; is used to
    assess the number of genomic copies per feature

nameColumn

double; which fraction of an interval needs to
    be included in a feature in order to count for the feature

fractionIncluded

one of <code>AlignedGenomeIntervals</code> or
    <code>integer</code>

returnType

logical; passed on to <code>fracOverlap</code> function,
    determines if overlap should be computed chromosome-wise, optionally
    distributed over several CPUs (with package <code>parallel</code>)

mem.friendly


  get the read counts for a supplied set of genomic features


manip

internal

The package 'girafe' deals with the genome-level
representation of aligned reads from next-generation sequencing
data. It contains an object class for enabling a detailed
description of genome intervals with aligned reads and
functions for comparing, visualising, exporting and working
with such intervals and the aligned reads. As such, the package
interacts with and provides a link between the packages
ShortRead, IRanges and genomeIntervals.

J Toedling

girafe

Genome Intervals and Read Alignments for Functional Exploration

getFeatureCounts function

<code>Genome_intervals</code> objects of genomic features

get the read counts for a supplied set of genomic features

getFeatureCounts: get the read counts for a supplied set of genomic features

Description

Usage

Arguments

Value

See Also