*** MACRO SECTION ***

*MACRO1

DEFINE MACRO1 (!POS !CHAREND ('/'))
  !DO !I !IN (!1)

COMPUTE !I = LG10(!I).

!DOEND
!ENDDEFINE.

*MACRO2

DEFINE MACRO2 (!POS !CHAREND ('/'))
  
  !DO !I !IN (!1)  

GET
    FILE='C:\Applied Biosystems\SDS Documents\temp0.SAV'.

* NonLinear Regression.
MODEL PROGRAM Fmax=1.2 Chalv=30 K=2.0 Fb=0 .
COMPUTE PRED_ = Fb + Fmax / (1 +2.7182818 ** (-(CYCLE -  Chalv ) / K) ).
NLR !I
  /OUTFILE='C:\Applied Biosystems\SDS Documents\temp1.SAV'
  /PRED PRED_
  /SAVE PRED_
  /CRITERIA SSCONVERGENCE 1E-8 PCON 1E-8 .
GRAPH
  /SCATTERPLOT(OVERLAY)=CYCLE CYCLE  WITH !I PRED_ (PAIR)
  /MISSING=LISTWISE .
EXECUTE.

ADD FILES FILE='C:\Applied Biosystems\SDS Documents\A_H.sav'
  /FILE='C:\Applied Biosystems\SDS Documents\temp1.sav'.
EXECUTE.
 
SAVE OUTFILE='C:\Applied Biosystems\SDS Documents\A_H.SAV'
  /COMPRESSED.

!DOEND
!ENDDEFINE.

*MACRO3

DEFINE MACRO3 ( ).
!DO !I =1 !TO 5.

SAVE OUTFILE='C:\Applied Biosystems\SDS Documents\TEMP3.SAV'
  /COMPRESSED.

SAVE OUTFILE='C:\Applied Biosystems\SDS Documents\TEMP4.SAV'
  /COMPRESSED.

ADD FILES FILE=*
  /FILE='C:\Applied Biosystems\SDS Documents\TEMP3.SAV'.
EXECUTE.

!DOEND.
!ENDDEFINE.

*** DATA IMPORT SECTION ***

GET DATA  /TYPE = TXT
 /FILE = 'C:\DATA\SDS EXPORT FILE.TXT'
 /DELCASE = LINE
 /DELIMITERS = "\t "
 /ARRANGEMENT = DELIMITED
 /FIRSTCASE = 3
 /IMPORTCASE = ALL
 /VARIABLES =
 V1 2X
 V2 3X
 V3 1X
 V4 10X
 V5 10X
 V6 10X
 V7 10X
 V8 10X
 V9 10X
 V10 10X
 V11 10X
 V12 10X
 V13 10X
 V14 10X
 V15 10X
 V16 10X
 V17 10X
 V18 10X
 V19 10X
 V20 10X
 V21 10X
 V22 10X
 V23 10X
 V24 10X
 V25 10X
 V26 10X
 V27 10X
 V28 10X
 V29 10X
 V30 10X
 V31 10X
 V32 10X
 V33 10X
 V34 10X
 V35 10X
 V36 10X
 V37 10X
 V38 10X
 V39 10X
 V40 10X
 V41 10X
 V42 10X
 V43 9X
 V44 10X
 V45 9X
 V46 10X
 V47 10X
 V48 10X
 V49 1X
 V50 F13.2
 V51 F13.2
 V52 F13.2
 V53 F13.2
 V54 F13.2
 V55 F13.2
 V56 F13.2
 V57 F13.2
 V58 F13.2
 V59 F14.2
 V60 F13.2
 V61 F13.2
 V62 F13.2
 V63 F13.2
 V64 F13.2
 V65 F13.2
 V66 F13.2
 V67 F13.2
 V68 F13.2
 V69 F13.2
 V70 F13.2
 V71 F13.2
 V72 F13.2
 V73 F13.2
 V74 F13.2
 V75 F13.2
 V76 F13.2
 V77 F13.2
 V78 F13.2
 V79 F13.2
 V80 F13.2
 V81 F13.2
 V82 F13.2
 V83 F13.2
 V84 F12.2
 V85 F13.2
 V86 F13.2
 V87 F13.2
 V88 F13.2
 V89 F13.2
 V90 F13.2
 V91 F13.2
 V92 F13.2
 V93 F13.2
 V94 F13.2
 .
CACHE.
EXECUTE.

MATCH FILES FILE=* /FILE= 'C:\APPLIED BIOSYSTEMS\SDS DOCUMENTS\CASELBL.SAV' .
EXECUTE.

FLIP
  VARIABLES= V50 TO V94  .

MATCH FILES FILE=* /FILE= 'C:\APPLIED BIOSYSTEMS\SDS DOCUMENTS\CYCLE.SAV' .
EXECUTE.

DELETE VARIABLES CASE_LBL . 

APPLY DICTIONARY FROM 'C:\APPLIED BIOSYSTEMS\SDS DOCUMENTS\DICT.SAV'.

*** CALCULATION OF CONVERSION FACTOR ***

GET
    FILE='C:\Applied Biosystems\SDS Documents\A_H1.SAV'.

SAVE OUTFILE='C:\Applied Biosystems\SDS Documents\A_H.SAV'.


MACRO2 A1 A2/.

SAVE OUTFILE='C:\Applied Biosystems\SDS Documents\TEMP5.SAV'
  /COMPRESSED.

COMPUTE F0 = Fmax / (1 + 2.718281828 ** (Chalv / K)) .
EXECUTE .

COMPUTE CF = 100000 / F0 .
EXECUTE.

SAVE OUTFILE='C:\Applied Biosystems\SDS Documents\TEMP3.SAV'
  /COMPRESSED.

GET
    FILE='C:\Applied Biosystems\SDS Documents\A_H1.SAV'.

SAVE OUTFILE='C:\Applied Biosystems\SDS Documents\A_H.SAV'
  /COMPRESSED.

MACRO2 A3 A4 /.

ADD FILES FILE='C:\Applied Biosystems\SDS Documents\TEMP5.SAV'
  /FILE='C:\Applied Biosystems\SDS Documents\A_H.SAV'.
EXECUTE.

SAVE OUTFILE='C:\Applied Biosystems\SDS Documents\TEMP5.SAV'
  /COMPRESSED.

GET
    FILE='C:\Applied Biosystems\SDS Documents\A_H.SAV'.

COMPUTE F0 = Fmax / (1 + 2.718281828 ** (Chalv / K)) .
EXECUTE .

COMPUTE CF = 1000 / F0 .
EXECUTE.

ADD FILES FILE=*
  /FILE='C:\Applied Biosystems\SDS Documents\TEMP3.SAV'.
EXECUTE.

FLIP
  VARIABLES= CF.

MACRO1 VAR001 VAR002 VAR003 VAR004 /.

EXECUTE.

COMPUTE CFmean = MEAN(var001,var002,var003,var004) .
EXECUTE .

COMPUTE CFmean = 10**(CFmean).
EXECUTE.

DELETE VARIABLES CASE_LBL VAR001 VAR002 VAR003 VAR004 .

SAVE OUTFILE='C:\Applied Biosystems\SDS Documents\TEMP3.SAV'
  /COMPRESSED.

SAVE OUTFILE='C:\Applied Biosystems\SDS Documents\TEMP4.SAV'
  /COMPRESSED.

ADD FILES FILE=*
  /FILE='C:\Applied Biosystems\SDS Documents\TEMP3.SAV'
  /FILE='C:\Applied Biosystems\SDS Documents\TEMP3.SAV'.
EXECUTE.

MACRO3.

SAVE OUTFILE='C:\Applied Biosystems\SDS Documents\TEMP3.SAV'
  /COMPRESSED.

Get
    FILE='C:\Applied Biosystems\SDS Documents\TEMP5.SAV'.

SAVE OUTFILE='C:\Applied Biosystems\SDS Documents\A_H.SAV'.

*** NLR ON REMAINING REACTIONS ***

MACRO2 A5 A6 A7 A8 A9 A10 A11 A12 /.
MACRO2 B1 B2 B3 B4 B5 B6 B7 B8 B9 B10 B11 B12 /.
MACRO2 C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 /.
MACRO2 D1 D2 D3 D4 D5 D6 D7 D8 D9 D10 D11 D12 /.
MACRO2 E1 E2 E3 E4 E5 E6 E7 E8 E9 E10 E11 E12 /.
MACRO2 F1 F2 F3 F4 F5 F6 F7 F8 F9 F10 F11 F12 /.
MACRO2 G1 G2 G3 G4 G5 G6 G7 G8 G9 G10 G11 G12 /.
MACRO2 H1 H2 H3 H4 H5 H6 H7 H8 H9 H10 H11 H12 /.

*** CALCULATION OF COPY NUMBER ESTIMATES ***

MATCH FILES FILE=* /FILE='C:\APPLIED BIOSYSTEMS\SDS DOCUMENTS\TEMP3.SAV'.
EXECUTE .

APPLY DICTIONARY FROM = 'C:\APPLIED BIOSYSTEMS\SDS DOCUMENTS\16digits.SAV'.

COMPUTE F0 = Fmax / (1 + 2.718281828 ** (Chalv / K)) .
EXECUTE .

COMPUTE CONC = F0 * CFmean.
EXECUTE .

APPLY DICTIONARY FROM = 'C:\APPLIED BIOSYSTEMS\SDS DOCUMENTS\SAMPLE.SAV'.

MATCH FILES FILE=* /FILE='C:\APPLIED BIOSYSTEMS\SDS DOCUMENTS\CASELBL.SAV'.
EXECUTE .

DELETE VARIABLES  V1 NCASES.

SAVE OUTFILE='C:\Applied Biosystems\SDS Documents\OUTPUT\A_H.SAV'.