geneTherapyPatientReportMaker

For a specific patient, report integration near oncogenes and potentially expanded clones across cell types and multiple time points. Abundance by default is based on unique fragment length.

Input

A csv file such as sampleName_GTSP.csv to describe the replicates and the samples.

head sampleName_GTSP.csv

sampleName,GTSP
GTSP0308-1,GTSP0308
GTSP0308-2,GTSP0308
GTSP0308-3,GTSP0308
GTSP0308-4,GTSP0308
GTSP0309-1,GTSP0309
GTSP0309-2,GTSP0309

#or 
Rscript path/to/check_patient_GTSP.R pFR03

sampleName,GTSP,patient
GTSP0308-1,GTSP0308,pFR03
GTSP0308-2,GTSP0308,pFR03
GTSP0308-3,GTSP0308,pFR03

• only sampleName, GTSP columns are necessary and the rest are ignored,
• the GTSPxxxx names must correspond to the same patient,
• the GTSPxxxx names must be in the specimen_management.gtsp database,
• all sites should be computed based on one reference genome.

Output

$trial.$patient.$today.html

Code example

• 1. check_patient_gtsp.R: get available datasets, generate a csv file for a patient

 Rscript path/to/check_patient_gtsp.R                    #get all processed samples
 Rscript path/to/check_patient_gtsp.R pFR03              #get data sets for patient pFR03 and output to csv format
 Rscript path/to/check_patient_gtsp.R pFR03 > pFR03.csv  #get data sets for patient pFR03 and output to tmp.csv

• 2. makeGeneTherapyPatientReport.R: generate report for a patient from the csv file

Rscript makeGeneTherapyPatientReport.R                     #read in sampleName_GTSP.csv by default
Rscript path/to/makeGeneTherapyPatientReport.R pFR03.csv   #generated above
Rscript path/to/makeGeneTherapyPatientReport.R pFR03.csv -s #determine abundance by sonicLength package (Berry, C. 2012)

• 3 check_gtsp_patient.R: get trial and patient information for the GTSPxxxx folders

Rscript path/to/makeGeneTherapyPatientReport.R                         #check current folder
Rscript path/to/makeGeneTherapyPatientReport.R  ~/Frances/run20150505  #check a run folder

Reference genome is specified by --ref_genome or -r option with default of hg18:

Rscript path/to/makeGeneTherapyPatientReport.R  ~/Frances/run20150505  --ref_genome hg19

To connect to databases .my.cnf should be present in ~ and group can be changed with --sites_group option with default of intsites_miseq for integration sites DB:

Rscript path/to/makeGeneTherapyPatientReport.R  ~/Frances/run20150505  --sites_group test_db

Metadata for GTSP is held in specimen_management DB and can be changed with --gtsp_group option with default "specimen_management":

Rscript path/to/makeGeneTherapyPatientReport.R  ~/Frances/run20150505  --gtsp_group gtsp_group_in_my_cnf

Once ref seq genes are downloaded from UCSC; data(genes and locations) are stored in refSeq.rds and this file can be used in future runs(to avoid downloading again):

Rscript path/to/makeGeneTherapyPatientReport.R  ~/Frances/run20150505  --ref_seq refSeq.rds

Database config file location

config file should be in home directory and called .my.cnf, e.g. ~/.my.cnf

The .my.cnf format is as follows:

[GROUP_NAME]
user=YYYYYYY
password=XXXXXX
host=microbYYYY.med.upenn.edu
port=3309
database=intsites_miseq

Dependencies

...

Testing

Run in the R console:

library(testthat)
test_dir(".")