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.
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 thespecimen_management.gtsp
database, - all sites should be computed based on one reference genome.
$trial.$patient.$today.html
-
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
-
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
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
...
Run in the R console:
library(testthat)
test_dir(".")