MANUAL FOR MING'S PROGRAM FILES

9/1/14

The first thing to do is open up the MATLAB folder which is stored under the folder
Ming in the common drive:

MATLAB should contain 4 subfolders, as shown above.

"Miscellaneous multi-use m-files" predominately contains scripts that were not written
for the purpose of being run independently. Instead it contains scripts which were written
as auxiliary functions to be called upon from within other bigger scripts stored in other
file directories (ie. RMS and TCGA).
"PPTs and Posters" has a copy of the poster I presented at Poster Day and the final data
presentation I made for our last morning lab meeting in August.
"RMS" contains everything relevant to the rhabdomyosarcoma samples, including script
m-files, output figures, segmentation files, etc. (See Part I on the next page.)
"TCGA- other cancers" contains everything relevant to the data taken of other common
adult cancers found on the broad institute website: http://gdac.broadinstitute.org/. (See
Part II of this manual.)

PART I- RMS
-----------------------------------------------------------------------------------------------------------When you open up the folder RMS, there should be 6 subfolders.

"Cytoband Location Spreadsheet" is where I saved the file delineating the chromosomal
locations (start and end) of each cytoband. This was accessed in several of the m-scripts
under "project m-files."
"Loci of CNV gains in normals" contains a word document listing all of the regions from
the 2500K fusion negative subset which had low copy number gains in many samples and
turned out (after searching the database at http://projects.tcag.ca/variation/) to be
confirmed CNVs.
"Outputs" contains a printout of all of the figure outputs of my m-scripts from "project mfiles."
"Project m-files" contains all of the in-house scripts I wrote relevant to RMS. (I will
elaborate on them shortly.)
"Segmentation spreadsheets" contains all of the segmentation files saved from Partek.
"Sorting sample groups" contains word documents that organize subsets of samples based
on conditions.

Project m-files:

The scripts are sorted into 6 categories, based on their functionalities.

a) The first folder, "colorband profiling" contains the script for the main colorful gui
which displays the intensity of the copy numbers of segments (according to files
generated in partek). The coloring is based on each segment's copy number's distance
from the mean (in terms of standard deviation). Auxiliary m-files display the genes within
the MCR for select regions and the amount of arm-level amplification for the select
regions.
b) The second folder "compare amp freq" contains the script that generates the graph
comparing the amplification frequencies of two chosen datasets (user does the choosing)
across an interval of copy number cutoffs.
c) The third folder compares the percentage of the arm that is considered amplified for
each arm (ie, 1p, 1q, 2p, 2q, etc) in two chosen datasets across an interval of copy
number cutoffs. It generates a 3D figure.
d) The fourth folder finds all of the amplification regions (besides 1p36, 2p24, 12q14,
13q14, and 13q31 in fusion positive) in a segmentation file as defined as a segment
having a copy number higher than a user-specified cutoff.
e) The fifth folder contains the scatterplot gui showing the distributions of the lengths of
segments and intensities of their copy numbers.
f) The sixth folder contains the ROC-generating script.
To run any and all of the m-scripts in MATLAB, make sure your current folder in the
MATLAB directory path is set to the folder called "MATLAB" under Ming and under the
common drive. The directory path is shown here:

Then, after this path is set to "MATLAB" under "Ming", go to the left hand side under the
tab "Current Folder" and right-click on "miscellaneous multi-use m-files." Select the
option "add to path" >> "select folders and subfolders."

Right-click on the folder "RMS" and do the same thing.

Then, to run a program, you can call the name of the function you wish to run directly in
the Command Window or you can double click on the .m file from its corresponding
folder. If you choose the second option, you can click "Run" on the top bar (see

screenshot below) and the program will run. Follow any instructions that follow and/or
make appropriate file selections and array density selections etc.