4DVOUS
VOUS annotation using 4D Genome data. The app takes a text file with genomic coordinates as input (chr:start-end format) and matches them against 4D Genome database in order to find chromatin interactions outside the regions. A screening of the ASD database is also implemented in order to test associations between mapped genes and autism-associated genes.
The app is developed in R with a Python style option parsing from the command line.
Requires R installed on the machine.
Usage: VOUS4D.R [options]
Options:
-c COORDINATES, --coordinates=COORDINATES
path to the text file with input coordinates in the format 'chr:start-stop'
-m CHARACTER, --method=CHARACTER
Choose overlapping method, options are: loose (match any region with overlaps >=1 BP), stringent (>50% overlap required). [default: loose]
-d CHARACTER, --database=CHARACTER
Path to the VOUS4D.db file, default assumes it is in the same folder
-a CHARACTER, --asd=CHARACTER
Perform match against ASD data? If TRUE an additional file ([outfile].ASD.txt) will be produced. [default: FALSE]
-o CHARACTER, --outfile=CHARACTER
Output file name '.txt' and '.xls' format are supported. [default: 4DG.out.txt]
-h, --help
Show this help message and exit
An example
$ Rscript ./VOUS4D.R --coordinates dummy.coordinates.txt --asd TRUE --out test.dummy.txt
=======================================================================
|| ||
|| Script developed by: Ferdinando Bonfiglio (nandobonf@gmail.com) ||
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=======================================================================
### Loading required packages... DONE!
### input coordinates:
|input.chr | input.start| input.end|
|:---------|-----------:|---------:|
|chr1 | 31584329| 31656511|
|chr16 | 100000| 110000|
|chr22 | 100000| 210000|
### Reading 4DGenome and ASD data... DONE!
### 25 interactions found in 4Genome
### Method: LOOSE overlap in H1ESC and 4 derived cells
### Method: removed 2 matches with both interactors overlapping input coordinates
### 7 unique genes mapped
### Method: removed matches without gene symbol annotation
### 7 input genes found in Genome-wide predictions of autism-associated genes (ASD)
### Top genes (ranked by q-value):
-------------------------------------------------------------------------------
genes cells methods score probability q-value
--------- ----------------- ----------------- --------- ------------- ---------
SERINC2 H1ESC IM-PET -0.9271 0.3325 0.01268
RHBDF1 H1ESC, H1 5C, IM-PET, -0.9238 0.3336 0.02095
derived IM-PET, IM-PET,
mesenchymal IM-PET, IM-PET,
stem cell, H1 IM-PET, IM-PET
derived
mesendoderm
cell, H1
derived
trophoblast,
H1ESC, H1
derived neural
progenitors, H1
derived
trophoblast, H1
derived
mesenchymal
stem cell
POLR3K H1 derived IM-PET, IM-PET, -0.9428 0.3297 0.1103
mesenchymal IM-PET, IM-PET
stem cell, H1
derived
trophoblast, H1
derived
mesendoderm
cell, H1ESC
-------------------------------------------------------------------------------
### ASD output file written to: test.dummy.ASD.txt
### 4D Genome output file written to: test.dummy.txt
### Analysis completed in 5.09094 seconds