The gamtools enrichment
tool is used to calculate the enrichment of pairwise
interactions between windows of different classes. For example, it can be used to
answer the question of whether a particular set of interactions connects windows
that contain genes with windows that contain enhancers more or less frequently
than would be expected by chance.
gamtools enrichment
requires two input files. The first is a tab-delimited table giving
the pairwise interactions. This table must contain the following columns:
Column | Description |
---|---|
chrom | Name of the chromosome |
Pos_A | index of the window on the left of the interaction |
Pos_B | index of the window on the right of the interaction |
interaction | strength of the interaction |
Window indices used for Pos_A and Pos_B are 0-based, such that 0
would be the first window on the chromosome and 20
would be the 19th. An
example file might look like:
chrom Pos_A Pos_B interaction chr1 10 20 0.75 chr2 10 20 0.50 chr1 10 30 0.40
The second input file is a comma-delimited (csv) table giving the classes of each window. This table can have the following columns:
Column | Description |
---|---|
chrom | Name of the chromosome |
i | index of the window |
start | Start co-ordinate of the window (optional) |
stop | Stop co-ordinate of the window (optional) |
Any additional columns will be interpreted as different classes. Each
class column should indicate whether the given window is a member of
the class with the values False
or True
. An example classification
table might look like this:
chrom,i,Enhancer,Gene chr1,10,True,False chr1,20,False,True chr2,20,True,False chr2,30,False,True
The output is a csv file in the following format:
Column | Description |
---|---|
class1 | First class involved in interaction |
class2 | Second class involved in interaction |
count | Number of interactions where a window in class1 interacts with a window in class2 |
permuted | Whether or not the interactions table was randomly permuted before counting |
For example:
class1,class2,count,permuted Gene,Gene,234148,yes Gene,Enhancer,268228,yes Enhancer,Enhancer,10598,yes
Usage:
gamtools enrichment [OPTIONS] -i <INTERACTIONS_FILE> -c <CLASSES_FILE>
Optional parameters:
Option | Description |
---|---|
-o, --output-prefix | First part of the output file name (default is "enrichment_results") |
-p, --permutations* | Number of times to randomly permute the input file |
-n, --no-permute* | Do not permute the input file, instead calculate observed counts |
* Options -p/-n are mutually exclusive, exactly one of these two options must be given