User Manual for csig for Windows
Contents
1. chrNum column decimal input filename location column log file making example output filename p valuel p valuez pi column pz column snpID column log output CS txt no output CS csv 0 03 005 RESULTS 030000 005000 000075 124939 0000685 0687 698 988750 987929 p2 p value TS logiO p value TS p value TSM 1logiO0 p value TSM TS value TSM value GO GO d O d OGO O csig exit successfully Thu Aug 7 23 50 34 2008 Total time elapsed O sec For Help press F1 Note using this exploration mode of csig exe cant indicate an output file to save the result You can use commandline redirect gt outputfile to capture or gt gt outputfile to accumulate the result Using commandline option o result txt here can allow user to make dedicated log filename e g log result txt in this Win32 gt is running example csig version 4 2 4 with options chrHum column decimal 6 input filename location column log file making example output Filename pua luel p value pi column pe column znpID column log output C amp txt N Batch Mode First to get the embedded example data sets total 3 by running csig with option e y or example yes Gould Hot Find G mulaork examples MESSAGE lt Making Sample Data Writing to testingy dat MESSAGE Making Sample Data 1HHH lines 5660 lines C myWork csig e y Writing to sample data22. 0 00000 6 42161 0 00000 6 46671 0 99920 0 99924 rS34221 4 43432 0 4332 0 005 0 06548 1 18392 0 05807 1 23604 0 66760 0 68515 Interpretation of output Columns Column head Explanation 1 SNPID SNP rs number user provided 2 Chr Chromosome number user provided 3 LOC SNP location user provided 4 pi p value 1 user provided 5 p2 p value 2 user provided 6 p value TS p value TS 7 l1og10 p value TS negative log10 of p value TS 8 p value TSM p value TSM 9 log10 p value TSM negative log10 of p value TSM 10 TS value Tail Strength Mean value 11 TSM value Tail Strength Median value Columns 6 and 8 are the composite p values and columns 7 and 9 are the log transformed version of the two composite p values Notice that this is a comma delimited file with csv file extension and thus user may click on it and let it automatically opened up in Excel and have better view or even take advantage of tools in Excel e g basic sorting and charting results In exploration mode the results are output to screen only but a log file will be generated which also contains result Another way to collect several runs of the exploration is to redirect the screen Output e g csig p1 0 233 p2 0 03 d 3 gt gt result explore txt DESCRIPTION This program csig is to calculate the composite significance combining both logistic regression p value and HWE testing p value Please refer to README PDF for rationale and detai
3. dat Weiting to zample data2 csu MESSAGE lt Making Sample Data Volume in drive C has no 1l 1 Then a screen on the right will show up The program terminates and lists the 3 example data sets sitting ina sub folder examples Volume Serial Number is Directory of G muMork e HR 87 2608 43 87 2688 43 87 2668 11 ii H Diris abel 3C9D 6646 xamples 317 testing dat 49 148 sample_data2 dat 238 655 sample_dataZ csyu 288 120 bytes 96 461 6604 860 bytes free 2 Now if you invoke this e y option again or accidentally use it in future while you ve already created the example data sets the program will pause to ask if you want to replace the existing ones E Composite Siginicance csig e y csig tversion 6 2 9 Win32 gt is running with options chrNum column decimal input filename location column log file making example output Filename p valuel p value pi column p2 column enpID column 6 log_out put_CS txt y WARNING lt Making Sample Data Example data may already exist Continue Cu n f If y is chosen new example data sets will be created Except for testing dat in the other two data sets the p values are generated by random although sample sizes are fixed see detail in the help manual by typing h or or see below Here is part of sample data2 dat bi pz snp O 074540633 7082386 0 0464276634156704 snpIDz u n 0 1
4. myWork 2 To explore the program type this C myWork csig p1 your p valuel p2 your p value2 decimal 3 where decimal 3 is optional if user desires to have output values with 3 decimal places And your p valuel and your p value are p value ML pi column p2 column sare csig version 4 2 9 Win3d2 gt is running the pair of p values from your logistic regression EEn ISTEME analysis and Hardy Weinberg Equilibrium test chrNum column order doesn t matter For example to calculate ST composite significance results using p value 1 ee og Fie Z jog output GE Ext 0 03 and another 0 005 use the following dc eee command p valuei z BH 83 FU DST ETE E 8 83 NEG LZ enpID column Upon pressing Enter the result will print to screen and be saved in a log file with default filename log_output_CS txt 830008 865006 Hipp 124939 Hia H68769 988 758 287929 pe pua lue TR EB Peh LA ad TER TTT TEE pua lue T amp SM L Pp H LATER TTS TSHM 1 1 TER T TSM value PS Pe Ee e en Se hc rio To view the log file you can either type more or write command with the filename The former will print the content on screen and the latter will launch Wordpad with the file content G Xmyullork write log output G amp 5 txt S Duk amp i amp 8 Running csig version 0 2 9 Win32 Thu Aug 7 23 50 34 2008 INPUT FILE INFO User provided options
5. us your suggestions Version 0 2 8 win32 Release 08 04 2008 History 08 07 2008 Modification Standardized prototyping of common subroutines Added another option yes to combine with example for silent support of overwriting any existing example data 08 04 2008 Development Release for other platforms Linux x86 32 tested on RedHat Fedora 8 SUSE 10 AMD x86 64 using 32 bit format Solaris SPARC 32 bit tested on SunOS 5 9 Generic 12230024 sun4u sparc SUNW Sun Fire 880 SunOS 5 10 Generic 127111 09 sun4u sparc SUNW Sun Fire V490 SunOS 5 10 Generic 120011 14 sun4u sparc SUNW Sun Fire 480R Modified output messages Changed heading by using log10 instead of neg log10 Revised the help manual message 15 R User Manual of csig exe version 0 29 07 31 2008 Fix allow leading for a real number in the input e g 001 for 0 001 change the name Pmean and Pmedian to o value TS and p value TSM in batch mode the default log file won t take the same file extension as the one of input data file as it did in the previous versions output file will always take csv to reflect its comma delimited format and force to take the advantage of easily being able to open in MS Excel since this is a Windows version 07 30 2008 Modifications embed example data into csig allowing user s choice to generate Two of the three examples are now ge
6. 3d2 gt is running with opts f examples testing dat o result_of_problem_data csv log file log_result_of_problem_data txt Checking the basic file properties counting lines 11 BASIC INFORMATION alue Filename stem testing Filename extension dat Fath examples File size Chute 31 amp File size 317 Bytes Total number of lines 11 Line size hyte gt 26 82 Line size 28 82 Bytes Last access time Fri Aug 8 66 18 37 268 Last modify time Fri Aug 8 86 16 37 268 Last inode chage time Thu Aug 7 23 59 15 268 permission PRINT FIRST 3 LINES OF examples testing dat SMPID Chr Loc pi p2 rs34221 1 23432 6 43532 86 681 re34222 1 23442 3 3e 5 8 681 Total error found Total lines dropped Total lines kept LIST OF DROPPED LINES B8 88 2068 1 889 loy nutput C amp txt H8 8 2068 2 456 log_result_of_problem_data txt B8 HB 2888 187 456 nutput GC amp 5 czu B8 H8 28B88 356 result_of_problem_data csy 4 Filets gt 114 877 bytes A Dirts gt 7 7 65 182 855 72H bytes free G Xmylork more result of problem data csu SHPID Chr Loc pi p2 p value TS I logyi1HCp value T8 1 p value TH log1B8Cp value T5H 1 TS vualue TS5M value rs34221 1 23492 8 4332 6 601 6 863133 1 199743 H Y B p TELE 1 255887 8 673666 8 691974 rz34222 1 23442 3 3e 5 H BH1 H x TR TS TS 5 5 6 421607 H HHBHBB H 6 466709 H 999288 8 999237 rs34221 4 43492 08 4332 6 60605 6 865475 1 183922 6 858671 1 236642 6 667
7. 54446224520553 0 40436440333724 snpIDZz di 0 008940959349274 64 O 390869622116771 snpIDz 04 O 01622 67098203301 O 511203425936401 snpIDz s O 279701946165594 0 125540100038052 snpIDZz ise 0 z2 68920272649646 O 13089247047901l2 snpIDZz zs5 nmzrmsmsada391137358 r nraa39rasamsm 2h ann Terns A ME CUIIPUSILE igiicancc 3 To avoid such a pause this version of eee csig exe supports a silent permission Geol of overwrite or abort of re creating chrNun column x input filename example data sets To overwrite use location column this beer ent p valuel ip ea C3 myWork csig e y y y bZ column snpID column 6 log_out put_CS txt y Or abort when previous make is Deleted file C myWork examples sample_data2 existing Deleted file C myWork examples sample_data2 Deleted file C myWork examples testing dat A subdirectory or file examples already exists C myWork csig e y y n MESSAGE lt Making Sample Data Writing to testing dat MESSAGE Making Sample Data Writing to sample data2 dat 1666 lines i MESSAGE Making Sample Data Writing to sample_data2 csu 58000 lines 4 fusing sample data2 dat for Volume in drive C has no label Volume Serial Number is 3C9D 6646 testing Now at prompt Directory of C myWork examples 68 68 2668 12 16 AM 317 testing dat 08 08 2008 12 16 AM 49 237 sample_data2 dat Ce myWork csig f 08 08 2008 12 16 AM 239 615 sample_data2 csv 3
8. 666 8 685146 D o CR User Manual of csig exe version0 2 9 oo Description This program is an implementation of the following methodology which has been published Wang J and Shete S A Test for Genetic Association that Incorporates Information about Deviation from Hardy Weinberg Proportions in Cases Volume 83 Issue 1 53 63 26 June 2008 Methodology For assessment of genetic association between single nucleotide polymorphisms SNPs and disease status the logistic regression model or generalized linear model is typically employed and has been applied to detect a variety of disease causing SNPs However the regression approaches do not integrate information that is available from other sources such as departure from Hardy Weinberg proportion in cases The Hardy Weinberg proportion is one of the most important principles in population genetics Deviation from Hardy Weinberg proportion among cases patients may provide additional evidence for the association between SNPs and diseases Thus testing for deviation from Hardy Weinberg proportion could be another approach for genetic association studies We developed two approaches 1 a mean based tail strength 7S measure and 2 a median based tail strength TSM measure to combine evidence from Hardy Weinberg proportion and from regression approaches to perform the case control association study Both measures combined two very different hypothesis tests the logistic
9. DONEIGUBE CONSOLE WINDOW saad eee eee ne ee eee nodu ps E Piu eli pacem edu sita 17 HOW TO QUICKLY CHANGE DIRECTORY TO A DESIRED DESTINATION IN CONSOLE WINDOW 18 o m Installation and uninstallation Installation This version is limited to Windows 2000 XP and Vista Installation can be done in the following steps Upon saving a copy of the program on your local machine click on csiaozerstaller exe and follow the on screen instructions ES Composite Significance 0 2 9 Setup m S Composite Significance 0 2 9 Setup m 1 Welcome to the Composite Significance 0 2 9 Setup Wizard License Agreement Please review the license terms before installing Composite Significance 0 2 9 267 This wizard will quide vou through the installation of Press Page Down to see the rest of the agreement Composite Significance 0 2 9 It is recommended that you close all other applications before starting Setup This will make it possible to update relevant system Files without having to reboot your computer Licensing Terms and Conditions IMPORTANT CAREFULLY READ THIS LICENSE BEFORE USING THIS PRODUCT USING THIS PRODUCT INDICATES YOUR ACKNOWLEDGMENT THAT YOU HAVE READ THIS LICENSE AND AGREE TO ITS TERMS IF YOU DO NOT AGREE DO NOT DOWNLOAD THIS PRODUCT LI T M D Anderson Cancer Center RESERVES THE RIGHT TO REQUEST THAT UNLICENSED LISERS DTSCONTTNI IF LISF OF AND DESTROY Al
10. File s gt 288 569 bytes examples sample data2 dat Dir s 96 457 404 416 bytes free c1 1 c2 2 d 7 This requests csig to take a sample data with one set of p values in column 1 option c1 1 and another in column 2 option c2 2 and the output result with 7 decimal places The screen will print out the one on the right And two files are generated a log file Log output CS txt and output CS csv 5 To view the result file type this C myWork write output CS csv bi p2 snp p value TS logiO0 p value TS p value TSM logiO0 p value TSM TS value TSM value 0 0745406337082386 0 0464276634156704 snpID2000 0 0093405 2 0296313 0 0102014 1 9913421 0 8744530 0 8680346 0 15244622528553 0 40436440333724 snpID2001 0 1676818 0 7755142 0 1747416 0 7576037 0 4680574 0 4538292 0 0089409593 4927464 0 390869622118771 snpID2004 0 0556926 1 2542024 0 0496267 1 3025375 0 6934363 0 7083503 0 0162267098203301 0 511203425936401 snpID2009 0 0965209 1 0064715 0 0887221 1 0519683 0 5922574 0 6108239 0 279701948165894 0 125540100038052 snpID2016 0 0939099 1 0272886 0 0994769 1 0022776 0 6019134 0 5879105 0 268928272649646 0 130892470479012 snpID2025 0 0938855 1 0274015 0 1002116 0 9990819 0 6019651 0 5863916 0 0720584439113736 0 0093390978872776 snpID2036 0 0027444 2 5615559 0 0026214 2 5814623 0 9319475 0 9331041 n nni ina7949845895672 n n010849222112447023 38nnT 2049 0 000000377 43 3242084 0 000nmm083859 4 34498578 0 9920289 n 992172 Ano
11. Maximize Close Edit Defaults Properties 2 Select tab Layout and change the value at Width in Screen Buffer Size The default is 80 c C MWMINDOM SS sysbem3z cmd exe Properties Options Font y Colors Window Preview C Screen Buffer Size Window Size Window Position Left 42 m Top v Let system position window Cancel 3 Upon click OK in the next dialog box check Save properties for future windows with the same title Then OK Ready to go Apply Properties E C Apply properties to current window only Y Save properties for future windows with same title KT donee T cid Cancel 17 How to quickly change directory to a desired destination in console window At console window using tab key for self completion has accelerated the typing for changing directory to a deep sit folder However it still takes quite a bit typing and tab key pressings In particular when the desired folder sits in another drive it may ask for one or two more steps Here lists a simple way to accomplish the task If the initial directory is at C drive when a console is just launched and a desired folder deeply sits at G drive the following steps may make it jump otep 1 With launched console and opened Windows Explore in your desired folder E Command Prompt o Back B ps Search lp Falders 555 AEL TEH eL osse Cn G volume2 work Compostesig
12. User Manual for csig for Windows Version 0 2 9 program implemented by Robert Yu theoretical methodology developed by Jian Wang and Sanjay Shete August 6 2008 si User Manual of csig exe version 0 2 9 Robert K Yu August 6 2008 easy computing with YU si User Manual of csig exe version 0 2 9 Robert K Yu rkyu gmdanderson org August 6 2008 Table of Contents INSTALLATION AND UNINSTALLATION ce eeeeeeee nennen enne nnn n nena n anna 4 MaE FA aa taa EAA EEA ATAA tan EA E E E E R E E A 4 NE ag e E E N A I EE A AEEA PAE AE A A A E AEE A TE 5 EIEE o UR EAA E AEAEE T T P EE EE M 6 Siaka wie Hes E A A nce gree R E ec ce eee 6 E TOR er e verse H TEE R R RR 7 Riad 0 ag to et e M 11 Jg elble Be ci Que MUDMME I MD D P p RU 11 DETAILED CSIG USAGE AND DESCRIPTION 1 eeeee erre e rennen nennen nnne nnns 11 dort E E 11 cid S ORT E 12 CAE Lug e 12 Bl p PP MPH 12 How are the random samples created isses nnns 13 DO PEETER EEN IEE EA A OH AE IAA O I EE AE A O VE EE jd xe HETP o 14 bzi deldudos Ge A PIC 14 4 0 17 HOW TO
13. any existing example data input file ist p value Ca real number 2nd p value fa real number column position of p valuel column position of p value output Filename Default is output_CS csu In the exploration mode this option will only affect log file name User can use redirect to capture the output in a file ecimal an integer representing the decimal place in output Effective numbers are BH to hut using BH would be meaningless although csig will take gt Default is 6 Use any number greater than csig will generate the maximum the current computer can express SYNOPSIS I GREATE example data files csig e y default is n This will generate 3 example data storing in examples sub directory finu value other than y will stop making examples If any example data exist from previous making You may press space bar to go through the pages or simply press Q to exit the message and it should stay at C You may start to explore or choose to quit the console to view the start menu of the installation EN our Windows sP Hg eeo irn Micro soft Office Tc ale fg Composite Significance M D Anderson Cancer Center wi B La spp nd Fi Microsoft Outlook with Business Contact Manager gt Aus Z Fi Microsoft Works gt EY Composite Significance Uninstall _ 7 Nikon View 6 d E Real Ti i Davin k At the start menu within Composit
14. c2 5 d 99 Note any value greater than 9 for option d allows csig to generate result values in max decimal places that the working computer can EXPLANATION I Making Example Data 12 Command csig e y will lead to create 3 example data And if csig detects prexisting examples it ll prompt for user s decision to generate new set replacing the old ones csig chooses to terminate upon this execution to allow user to choose examples for the next run Except for testing dat the other two are generated using random numbers Thus each run may have different value sets How are the random samples created sample data2 dat containing 1000 lines uses double random for p value 1 and p value 2 i e p valuel rand rand 1 5 3 p value2 rand rand sample data2 o5v Containing 5000 lines uses the following for p value 1 and p value 2 1 e p valuel rand 0 02 p value2 rand rand 0 1 Il Data input 1 For exploration user just needs to give a pair of p values and or output decimal place requirement e g csig pl 0 023 p2 1 05e 3 d 3 If option d is not provided a default 6 will be used Any number greater than 9 will direct csig to generate whatever the computer may be able to express 2 For batch mode user is required to provide the list of p value pairs in a data file using either or space including tab or mixture of both as delimiter and then tel
15. e Significance you have a manual folder containing README pdf serving as user guide this document Composite Significance shortcut link to launch console window Uninstall will allow you easily remove all install files without your looking for separately A link to M D Anderson Cancer Center provides a convenience to visit its website Uninstallation To remove the installation go to Start Programs Composite Significance Uninstall It ll delete all the files and programs Composite Significance 0 2 9 Uninstall Note after installations csig exe is physically sitting in C NWINDOWS Address CiWIMDOWS Mame Size Type Date Modified csig exe 1 161 KB Application 6712006 11 04 PM from where user can directly invoke it without setting it in the path If you have your own working directory in path such as c Nbin you may create a copy of csig exe there And you can use it without any links in the start menu But if the installation was done through the installer it d be better not to change the file location otherwise it ll make later uninstallation problematic Get started Exploration Mode Before start it might benefit to know how to configure console window in appendix E Composite Siginicance CiN mkdir myWork CS 5c0 myllork LSD E el 1 Start gt Programs gt Composite Significance to invoke the console Then make and change to a working folder e g c
16. l csig where are the column positions for p valuel and p value2 One example is SNFPID UChr Lhoc pl ps rs34221 1 23432 0 4332 0 001 rSs34222 1 23442 3 3e 5 0 001 rs34223 1 23452 1 56332 p32 rs34224 1 23462 0 5674 rs34221 4 43432 0 4332 0 005 rs674222 5 33442 1 2e 15 3 051 pag924223 6l 73452 1 2332 p2 rs764224 z 83462 0 1332 rs764224 x 83462 0 1332 a NL e AX 83462 2 0 1334 where pl and p2 are in columns 4 and 5 and the first 3 columns are optional SNP info But notice that a header line is always expected This dataset was created on purpose with mixed types of delimiter i e and and 13 Also some invalid p values were added to test whether csig will detect Upon detected the entire SNP line will be dropped but continues to process the next line To run csig with this dataset if saved as data dat the commandline typing would look like this csig f data dat cl 4 c2 5 o result csv d 5 Ill Output And two output files will be generated one result file result csv and a log tile log result Ext The log file will list total drops of 8 lines including the header lines for analysis and keep 3 valid lines for output results In result csv the result looks like this SNPID Chr Loc pl b2 p value Ts logl0 p TS l p valus TSM l logi10 p TSM I TS valus TSM valus r5320221 21 423432 U 4332 U0 001 0 06313 1 199574 0 05558 1 255095 0 07300 0 595157 rS34222 1 23442 3 3e6 5 0 001
17. l v Click Next to continue If you accept the terms of the agreement select the first option below You must accept the agreement to install Composite Significance 0 2 9 Click Next to continue G Composite Significance 0 2 9 Setup J LC Composite Significance 0 2 9 Setup Choose Install Location Installing Choose the Folder in which to install Composite Significance 0 2 9 26 Please wait while Composite Significance 0 2 9 is being installed 2 Setup will install Composite Significance 0 2 9 in the Following Folder To install in a different Extract csig exe Folder click Browse and select another Folder Click Install to start the installation Output Folder C YWINDOWS Extract csig exe Destination Folder C Program Files Composite Significance Space required 1 9MB Space available 89 8GB Completing the Composite Significance 0 2 9 Setup Wizard Composite Significance 0 2 9 has been installed on your computer Click Finish to close this wizard If the checkbox was checked on the last screen above a console window with help message will pop up E Composite Siginicance 3 IS x USAGE csig optioni option 1 y version show version h i help show this message m man show this message i example making embedded example data i YES combined with e to give a silent support of overwriting
18. led information of this methodology or email to authors below 14 R User Manual of csig exe version 0 29 Dr Sanjay Shete sshete mdanderson org Dr Jian Wang jianwang mdanderson org Reference Wang J and Shete S A Test for Genetic Association that Incorporates Information about Deviation from Hardy Weinberg Proportions in Cases Volume 83 Issue 1 53 63 26 June 2008 csig was designed to facilitate the calculation of this method for both exploration purpose and batch mode processing need Note According to the simulation studies in the paper we can see that the empirical p values from the permutation approach and the exact p values from the exact formulas are very similar and the exact formulas give slightly conservative p values Therefore the exact p values are considered satisfactory The current version of this computer program only applies to calculation of the p values using the exact formulas The program for the permutation method as described in the paper is under construction and will be available soon csig version 0 2 8 win32 was designed as a analysis module in our ongoing programming effort to create a SNP Analytics which is a GUI based software That software will integrate other tools including LD measurements exact HWE test haplotype estimation SNP simulation association tests etc Please send us your email address and we will update our new tools or tell
19. nerated with randomness see details in manual Windows installer thus changes accordingly no link to example files at start menu Meanwhile improvement on invoking console made Fixed some typos in PDF user manual Changed heading by using neg log10 instead of log10 The latter would have to cause problem if user open the csv file in MS Excel which has trouble to decipher the leading n n Sign Added an alarm bell at the end of csig It ll ring only when it runs over 2 seconds This may be helpful when longer input data file is fed 07 29 2008 Modifications allow flexible column positions of p values allow user indication of output decimal place 07 13 2008 Initial release single module calculating composite significance Further questions or reporting bugs please email Robert Yu at rkyu mdanderson org 16 o CB User Manual of csig exe version 0 2 9 o Appendix How to configure console window The default setting of the Windows console window may not be well fit your commandline program e g lower screen buffer size etc The set it wider for example you can follow the steps below and you may choose to adjust other properties too Upon the console window is up running e g Start gt run gt cmd or through launching Composite Significance program do the following 1 Right click the top title bar and choose Properties c CA WINDOWS sys Restore Move Size Minimize O
20. nficanceO80625 Csignficancetreleasetze M EJ 6 C Copyright 1985 2881 Microsoft Corp ddress 17 GarWalume2YworklCompositeSignificanceQ8D625 Csignificancelrelease029 v 0 sx l Mame Size Type Date Mo C Documents and Settings Robert gt File and Folder Tasks Z aep File Folder 51712008 G Make a new folder E 4README dac 1KB Microsoft 8 7 2008 A E E A 6 CSignificance pl 31KB PL File Brzrz d8 Web CSignificance pl bak 31 KB BAK File arz 12008 E Share this folder B README doc 563KB Microsoft 712008 Step 2 Highlight and copy the path at the Address bar in Windows Explorer Note the Copy step can be done either using right click on the highlighted path or pressing Ctl C and Folder Tasks examples i Cut i Make a new Folder README doc LKB Mig COPY i E Je CSignificance pl 31 KB PL Paste id M ad CSigniFicance pl bal 3ikB BA Delete Share this Folder Bi README doc S63 KB Mi Select All Step 3 At console prompt type cd d and at the console title bar right click and choose Edit Paste E Command Prompt Microsoft Windows KP Version 5 1 2668 GC Copyright 19865 2601 Microsoft Corp Move Size Restore C Documents and Settings Robert cd sd Minimize Maximize X Close Edit Defaults Properties Mark Copy Enter Paste Notice that switch d for cd is critical when a directory change is attempted from one drive to ano
21. p value a real number p2 2nd p value a real number cl column position of p valuel 11 User Manual of csig exe version 0 29 LLL C2 column position of p value2 o outp output filename Default is OUtput CS cgy In the exploration mode this option will only affect log file name User can use redirect to capture the output in a file d decimal an integer representing the decimal place in output Effective numbers are 0 to 9 but using O would be meaningless although csig will take Default is 6 Use any number greater than 9 csig will generate the maximum the current Computer Can express SYNOPSIS I CREATE example data files csig e y default is n This will generate 3 example data storing in examples sub directory Any value other than y will stop making examples If any example data exist from previous making csig will pause a question for permission of replacement A negative answer will abort the Step and continue to use the current ones A silent permission can provide at initial starting of csig instead of waiting for response csig e y y y TI EXPLORATION with a pair of p values csig pl 0 002 p2 1 2e 5 Note the p value in dot leading format is also acceptable e g 002 for 0 002 csig pl 002 p2 0 03 Or csig pl 0 002 p2 1 2e 5 d 3 gt output txt III BATCH MODE of list of p value pairs in file csig f sample data dat o result txt c1 4
22. regression model and the test for deviation from Hardy Weinberg proportion in cases and allowed dependence between these two tests The newly developed approaches are more powerful than the traditional association study approaches achieving higher power than each individual test and maintaining good control over type error probabilities We derived the exact formulas for calculation of corresponding p values We also proposed an approach for estimating empirical p values with the use of a resampling procedure For the detail of the approaches please refer to the study of Wang and Shete Note According to the simulation studies in the paper we can see that the empirical p values from the permutation approach and the exact p values from the exact formulas are very similar and the exact formulas give slightly conservative p values Therefore the exact p values are considered satisfactory The current version of this computer program only applies to calculation of the p values using the exact formulas The program for the permutation method as described in the paper is under construction and will be available soon Detailed CSig Usage and Description USAGE csig optionl option2 V version show version h help show this message m man show this message e example making embedded example data y yes combined with e to give a silent support of overwriting any existing example data f file input file p1 1st
23. st for this purpose Here is what the data looks like ENPID Chr Loc p1 p2 rs34221 1 23432 0 4332 0 001 rs34222 1 23442 3 3e 5 0 001 rs34223 1 23452 1 56332 p2 rs34224 1 23462 0 5674 rs34221 4 43432 0 4332 0 005 rs574222 5 33442 1 2 amp 8 15 3 051 rs994223 61 73452 1 4332 p2 rs764224 z 83462 0 1332 rs764224 x 83462 D 1332 rs754224 XY 83462 2 0 1332 The data has p values pairs in columns 4 and 5 Some of them either containing one p value or containing non number Also notice the mixture of the delimiters not only mixing with spaces tabs but also some comma comes with space before and or after it But csig can detect and process them properly Run this following command csig f examples testing dat c2 5 cl 4 o result of problem data txt where o option indicates user defined output filename Although it contains txt extension the program changes it to csv After executing the command the screen and log file both report the finding of errors and how many error lines were dropped and how many valid lines yield the results GY Composite Siginicance csig version 6 2 9 Win32 gt is running with options chrHum column decimal input filename location column log file making example output filename p valuel p value2 pi column HZ column enpID column 6 examples testing dat loy output GC amp txt no result_of_problem_data txt 4 G csig version 4 2 9 Win
24. ther Step 4 Press Enter Done EY Command Prompt ol N Microsoft Windows AF Version 5 1 26606 CC Copyright 1985 2601 Microsoft Corp C Documents and Settings Robert cd zd G Uolume2 swork CompositeSignif icanceb 625 C8 ignif icance re ET E R Pe GS U o lume work Compos ites ignif 1C anc eai Qp ZR xC ignif icance re lease gt 18
25. ther way to view the result is to open it up in MS Excel where user may take advantage of tools Excel provides e g sorting and charting etc To open it in Excel just go to the working folder and directly click on output CS csv file A quick way to go to the current working folder user may type at the prompt the following C myWork start Coxmyllork gt start Address C Cimy Work Date Modified 6 5 2008 12 10 AM sfe 2008 12 15 AM 5 5 2008 12 15 AM SIze Type File Folder ZKD Text Document 107 KB Microsoft Excel B lag output C5 ExE output CS csv Notice a little dot after start Ad fe pl A B C D E F E H E Ip snp p value TS oqt p value T53J p value_TSh ogt p alue TS TS value TEM value 2 0074540634 0 046427663 snplD2000 0 0093405 202963135 0 0102014 1 8813421 0 674453 8680348 3 0152445225 0404364403 snplD2001 0 16765818 7755142 0A747416 7576 037 04680574 O 4538292 4 0008940959 0 380869522 snplD2 004 0 0556926 12542024 0 0498267 1 5025375 O 6934365 7083503 5 D 01622671 0 511203426 snplb2009 0 0985209 10064715 0 0887221 0519683 O 592357 4 0 6108239 b 0279701948 0 1255401 SnpiD201 0 0939099 10272866 0 0994769 0022776 5019134 58731 5 T n EGG TT 3 r 4d anem dT rel mE n PTG GE E 4 nT dnd E n 30784 4 c AS A rn CNA NDESA n colconm4c 6 Now you may test how csig detects and treats errors in the input data set Example data file testing dat was provided ju
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