CMDS
By Qunyuan Zhang, 02/05/2009
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Create a working DIR
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Copy the R files below to your working DIR
cmds_broad.R
cmds_focal.R
cmds_lib.R -
Prepare copy number data files in a data DIR (only data, don't include any other files in the data DIR)
Each chromosome (or each chromosomal arm) for all samples is saved to a TAB delimited file. The names of columns 1 and 2 (i.e. chromosome and position) are fixed, don't change them. The CN values can be either log2 ratio or estimated copy number like 1.5, 2.1, 3.2 ..... Please refer to the file example_data.txt
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Modify the line below in cmds_focal.R
data.dir="your_data_DIR"
which specifies your data DIR -
Run cmds_focal.R (focal region test)
In single machine mode:
R --no-save < cmds_test.R (this may take 1 or 2 hours)Or in cluster mode:
bsub "R --no-save < cmds_focal.R 1"
bsub "R --no-save < cmds_focal.R 2"
bsub "R --no-save < cmds_focal.R 3"
bsub "R --no-save < cmds_focal.R 4"
...
the number of jobs depends on the number of data filesTwo result DIRs below will be created in your working DIR:
focal/
focal_plot/(Cluster mode may not produce graphs in the dir focal_plot/)
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Run smds_broad.R (broad region test, only can be run after step 5 has been finished)
R --no-save < cmds_broad.RTwo summarized files and two result DIRs below will be created in your working DIR:
cmdsFocaldAll.txt (focal region test)
cmdsBroadAll.txt (broad region test, in development)
broad/
broad_plot/The two summarized files contain all info from result DIRs focal/ and broad/ (the difference is the DIRs give the results chromosome by chromosome)
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plot_ALL.R and plot.R can be used to produce graphs.
