how to caculate the K module?

[zifeng9527]

Thanks for your software.

According to your Genome Research paper, I know that you caculated the K modules (subpopulation) using the script in "TFTG_co_module.m" and the TRS matrix. However, in your TimeReg manual, there is no item to tell us how to use this script. I'm a layman on matlab. Can you illustrate how to get the K using your script?

[Chloe-Thangavelu]

##HELP SECTION##
I don't know how to set the K-value (it looks like in the paper they try several k-values and pick the best one)
But here is some info for those who can't read matlab or may need help.

For default settings:
Set Pre-processing to 1
Set K to above 1 to get all outputs

Here is the config file I used:
PECA_Module_dir = './.';
Expfile='./testData/Exp.txt';
sample_trs_files='./testData/test_trs_info1';
TFName_file='./testData/TFName.txt';
TGName_file='./testData/TGName.txt';
Outdir='./testData/out10312022';
pre_process_required=1;
species = 'mouse';
lambda=0.2;
K=[1,1,1,1,2];

otherwise you might get the following error or you might not get all your output files.

Error:
Error using nnmf>checkmatrices (line 353)
A must be a matrix of numeric values.

Error in nnmf (line 115)
checkmatrices(a,w0,h0,k);

Error in TFTG_co_module (line 20)
[W,H]=nnmf(ZZ,k,'algorithm','mult','replicates',10,'options',opt);

Error in timeCourse_PECA_module (line 6)
[TFCluster1{1,ii},TGCluster1{1,ii},W{1,ii},H{1,ii},p1{1,ii},p2{1,ii},FC1{1,ii},FC2{1,ii},ZZ{1,ii}]=TFTG_co_module(TRS_norm{1,ii},R,TFName,Symbol,K(ii),Exp2(:,ii));

Error in run_TCRA (line 71)
[TFCluster1,TGCluster1,DriverTF,match]=timeCourse_PECA_module(TRS_norm,Exp,Exp2,TGName,Sample,TFTG_corr_public,TFTG_corr_private,lambda,TFName,TFExp,K,Outdir);

Solution: Set Preprocessing to 1