Genomic Heatmap Maker for Integration Sites

Script to run genomic heatmap maker for sites from DB

For list of samples and sample replicates generate heatmap for a given reference genome and given integration site database:

Rscript genomic_heatmap_from_db.R sampleName_GTSP.csv -o heatmap --ref_genome hg18  --sites_group intSitesDev237

Group should be present in ~/.my.cnf.

File sampleName_GTSP.csv should have at least 2 columns: sampleName and GTSP. sampleName is the name used in integration sites db. If column label is given it will be used as a label in heatmap, otherwise GTSP column will be used. All samples with the same GTSP column merged together. See geneTherapyPatientReportMaker 'check_patient_gtsp.R' script for instruction how to generate sampleName_GTSP.csv for samples that are in speciment management db.

Database configuration file

Configuration file should be in home directory and called .my.cnf, (~/.my.cnf).

Dependencies

intSiteRetriever hiAnnotator pipeUtils colorspace GCcontent

At present genomes hg18 and mm9 genomes added, if other genomes are used add them to genomicHeatmapMaker.R.

Implementation details: pipeUtils requirement

needs a column type which is hard-coded as "insertion" for integration site and "match" for match random contol(mrc).

pipeUtils can only generate figures for 2 or more samples.