neuroblastoma

Tumors from patients at the Institut Curie were assayed using array
 comparative genomic hybridization.
 Their normalized copy number profiles are available
as <code>neuroblastoma$profiles</code> and the breakpoint annotations are available
as <code>neuroblastoma$annotations</code>.

datasets

Annotated neuroblastoma copy number profiles,
a benchmark data set for change-point detection algorithms,
as described by Hocking et al. <doi:10.1186/1471-2105-14-164>.

Toby Hocking

Neuroblastoma Copy Number Profiles

Toby Dylan Hocking

neuroblastoma function

A named list of 2 data frames:<dl>
 <dt><code>profiles</code></dt>
<dd>A data.frame with
 one row for each probe, and
 these variables:<dl>
 <dt><code>profile.id</code></dt>
<dd>factor: id of copy number profile.</dd> <dt><code>chromosome</code></dt>
<dd>factor: chromosome on which the probe was mapped.</dd> <dt><code>position</code></dt>
<dd>integer: probe was mapped to this position
	in base pairs.</dd> <dt><code>logratio</code></dt>
<dd>numeric: normalized logratio of the probe,
	which should be
	proportional to copy number.</dd> 
</dl></dd> <dt><code>annotations</code></dt>
<dd>a data.frame with
 one row for each annotated region,
 and these variables:<dl>
 <dt><code>profile.id</code></dt>
<dd>factor: id of copy number profile.</dd></dl></dd> <dt><code>chromosome</code></dt>
<dd>factor: chromosome of this annotation.</dd> <dt><code>min</code></dt>
<dd>integer: lower limit of this region in base pairs.</dd> <dt><code>max</code></dt>
<dd>integer: upper limit of this region in base pairs.</dd> <dt><code>annotation</code></dt>
<dd>factor: annotation of this region,
	either <code>"normal"</code> for no breakpoints or
	<code>"breakpoint"</code>
	for at least one breakpoint.</dd> 
</dl>

Format

Neuroblastoma copy number profiles and breakpoint annotations — neuroblastoma

A named list of 2 data frames:<dl>
 <dt><code>profiles</code></dt>
<dd>A data.frame with
 one row for each probe, and
 these variables:<dl>
 <dt><code>profile.id</code></dt>
<dd>factor: id of copy number profile.</dd>

 <dt><code>chromosome</code></dt>
<dd>factor: chromosome on which the probe was mapped.</dd>

 <dt><code>position</code></dt>
<dd>integer: probe was mapped to this position
	in base pairs.</dd>

 <dt><code>logratio</code></dt>
<dd>numeric: normalized logratio of the probe,
	which should be
	proportional to copy number.</dd>

 
</dl></dd>

 <dt><code>annotations</code></dt>
<dd>a data.frame with
 one row for each annotated region,
 and these variables:<dl>
 <dt><code>profile.id</code></dt>
<dd>factor: id of copy number profile.</dd>

 <dt><code>chromosome</code></dt>
<dd>factor: chromosome of this annotation.</dd>

 <dt><code>min</code></dt>
<dd>integer: lower limit of this region in base pairs.</dd>

 <dt><code>max</code></dt>
<dd>integer: upper limit of this region in base pairs.</dd>

 <dt><code>annotation</code></dt>
<dd>factor: annotation of this region,
	either <code>"normal"</code> for no breakpoints or
	<code>"breakpoint"</code>
	for at least one breakpoint.</dd>

 
</dl></dd>

 
</dl>

neuroblastoma: Neuroblastoma copy number profiles and breakpoint annotations

Description

Usage

Arguments

Format