General file hierarchy
The RGT-Viz requires a main directory name (e.g. project_A) and a title for the current test (e.g. projection_test_1). It allows the user to perform various tests under the same project and save them under the same directory. The example below shows the way
---> project_A |----> projection_test_1: html, pdf, png... | |----> projection_test_2: html, pdf, png... | |----> intersection_test_1: html, pdf, png...
Category 1: Tests for regions versus regions
There are two sets of BED files, which you want to compare with and evaluate their association between the other: the reference and the query. They have different experimental matrices as following:
Reference experimental matrix (em_ref.txt)
name type file ref1 regions ./ref1.bed ref2 regions ./ref2.bed
Query experimental matrix (em_que.txt)
name type file que1 regions ./que1.bed que2 regions ./que2.bed que3 regions ./que3.bed
For performing projection test on these BED files, the command is as below:
rgt-viz projection -r em_ref.txt -q em_que.txt project_A
The projection test is performed on the given reference (em_ref.txt) and the given query (em_que.txt) under the project name project_A. The default title for projection test is: projection_test.
Changing the title:
rgt-viz projection -r em_ref.txt -q em_que.txt project_A -t projection_1203
Changing organism (default is hg19) to mm9:
rgt-viz projection -r em_ref.txt -q em_que.txt project_A -organism mm9