Install PCGP packages

We are currently offering a beta version of an application programming interface for R (http://www.r-project.org) which can be installed using the instruction below.

Use the PCGP.R script to install PCGP packages [PCGPDataAPI version 0.4 (beta version)].

To install a particular package, e.g., PCGPDataAPI, type (or copy and paste) the following in an R command window
source("http://explore.pediatriccancergenomeproject.org/PCGP.R");
pcgpinstall("PCGPDataAPI")
Once installed simply add the following line to the beginning of your scripts.
require("PCGPDataAPI")

Examples of usage

Get all structural variants for all patients
getPCGPdata(datatype="sv")
Get all structural variants for a single sample
getPCGPdata("SJTALL001", datatype="sv")
Get all copy number changes for a single sample
getPCGPdata("SJTALL001", datatype="cnv")
Get all single nucleotide variations and insertions/deletions for a single sample
getPCGPdata("SJTALL001", datatype="snv_indel")
Draw a circos plot of a selected sample
drawPCGPcircos("SJTALL001")
Draw a circos plot of a selected sample next to your custom graph
dev.new (width=10, height=5);
par (mfcol=c(1,2));
drawPCGPcircos("SJTALL001");
plot (rnorm(100))
Get all data for a Gene Symbol
getPCGPgenedata("EZH2")
Get a sample listing with disease information
getPCGPsamplelist()
If you are interested in repackaging PCGPDataAPI on other platforms, please download the source code using this link PCGP Data API Source Code

PCGP Explore - What's New

Click here to view Release Notes
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