sample_df

control_df


These two mass spec data sets are the experiment and control results from a 
mass spec of a GREB1 ChIP (sample_df) and an IgG ChIP (control_df).


datasets

The output of an affinity-purification mass spectrometry
experiment is typically a list of proteins that were observed
in the experiment, identified by UniProt identifiers
(http://www.uniprot.org/).  This package takes as input a list of
UniProt identifiers, and the associated Mascot scores from the
experiment (which indicate the likelihood that the protein has
been correctly identified), clusters them by gene ontology
category (http://geneontology.org/), then draws diagrams
showing the results in hierarchical clusters by category, with lines
for individual proteins representing the associated Mascot score.
The results are in general not publication-ready, but will rather
require editing via a graphics editor that can interpret SVG (scalable
vector graphics) format.  As an alternative representation, the
package will also generate tag clouds based on the Mascot scores.

Gord Brown

msarc

Draw Diagrams (mis)Representing the Results of Mass Spec
Experiments

sample_df function

Data frames with the following 3 columns:
  <dl>
    <dt><code>uniprot</code></dt><dd>the UniProt ID of the protein</dd> <dt><code>id</code></dt><dd>the symbolic name of the protein</dd> <dt><code>score</code></dt><dd>the MASCOT score of the protein</dd> </dl> 

Format

From Mohammed, H., D'Santos, C., Serandour, A. A., Ali, H. R., Brown, G. D., Atkins, A., et al. (2013). Endogenous Purification Reveals GREB1 as a Key Estrogen Receptor Regulatory Factor. Cell reports, 3(2), 342-349. doi:10.1016/j.celrep.2013.01.010

sample_df: Sample Data for the msarc Package

Description

Usage

Arguments

Format

Source

Examples