Subscribe Bookmark RSS Feed

Haplotype Regression

maclines0

Community Member

Joined:

Dec 15, 2015

I am running the haplotype regression function and am unclear exactly how to interpret the output files. What I am most interested in is determining the trait mean for each haplotype. In the SAS output window I am given estimate values for each haplotype. These values are all negative for all haplotypes in the overall test while some are negative for some haplotypes and positive for others in the individual tests. Any help would be appreciated. I attached the output below:

----------------------------------------------------------------------------------------------------

                                                            Overall Test                         16:33 Monday, February 29, 2016  20

------------------------------------------------------------- Window=1 -------------------------------------------------------------

                                                         The GLM Procedure

                                              Number of Observations Read         132

                                              Number of Observations Used         132

----------------------------------------------------------------------------------------------------

                                                            Overall Test                         16:33 Monday, February 29, 2016  21

------------------------------------------------------------- Window=1 -------------------------------------------------------------

                                                         The GLM Procedure

                                                  Dependent Variable: PSS_2013  

                                                                Sum of

                        Source                      DF         Squares     Mean Square    F Value    Pr > F

                        Model                        7      0.57061574      0.08151653       5.13    <.0001

                        Error                      124      1.97091759      0.01589450                    

                        Corrected Total            131      2.54153333                                    

                                       R-Square     Coeff Var      Root MSE    PSS_2013 Mean

                                       0.224516      59.09690      0.126073         0.213333

                        Source                      DF       Type I SS     Mean Square    F Value    Pr > F

                        H1                           1      0.04265381      0.04265381       2.68    0.1039

                        H2                           1      0.01099720      0.01099720       0.69    0.4071

                        H3                           1      0.15427488      0.15427488       9.71    0.0023

                        H4                           1      0.15181720      0.15181720       9.55    0.0025

                        H5                           1      0.13429041      0.13429041       8.45    0.0043

                        H6                           1      0.07494326      0.07494326       4.72    0.0318

                        H7                           1      0.00163899      0.00163899       0.10    0.7487

                        Source                      DF     Type III SS     Mean Square    F Value    Pr > F

                        H1                           1      0.00756075      0.00756075       0.48    0.4917

                        H2                           1      0.03763456      0.03763456       2.37    0.1264

                        H3                           1      0.29761793      0.29761793      18.72    <.0001

                        H4                           1      0.24398325      0.24398325      15.35    0.0001

                        H5                           1      0.17124082      0.17124082      10.77    0.0013

                        H6                           1      0.07487811      0.07487811       4.71    0.0319

                        H7                           1      0.00163899      0.00163899       0.10    0.7487

                        Contrast                    DF     Contrast SS     Mean Square    F Value    Pr > F

                        Overall                      7      0.57061574      0.08151653       5.13    <.0001

                                                                   Standard

                                 Parameter         Estimate           Error    t Value    Pr > |t|

                                 Intercept     0.2890451760      0.02424577      11.92      <.0001

                                 H1            -.0302601288      0.04387445      -0.69      0.4917

                                 H2            -.0674181711      0.04381340      -1.54      0.1264

                                 H3            -.1993103565      0.04605998      -4.33      <.0001

                                 H4            -.2019650826      0.05154893      -3.92      0.0001

                                 H5            -.1608493234      0.04900484      -3.28      0.0013

                                 H6            -.1115559265      0.05139710      -2.17      0.0319

----------------------------------------------------------------------------------------------------

                                                            Overall Test                         16:33 Monday, February 29, 2016  22

------------------------------------------------------------- Window=1 -------------------------------------------------------------

                                                         The GLM Procedure

                                                  Dependent Variable: PSS_2013  

                                                                   Standard

                                 Parameter         Estimate           Error    t Value    Pr > |t|

                                 H7            -.0151106871      0.04705650      -0.32      0.7487

----------------------------------------------------------------------------------------------------

                                                        Test for Haplotype 1                     16:33 Monday, February 29, 2016  23

------------------------------------------------------------- Window=1 -------------------------------------------------------------

                                                         The GLM Procedure

                                              Number of Observations Read         132

                                              Number of Observations Used         132

----------------------------------------------------------------------------------------------------

                                                        Test for Haplotype 1                     16:33 Monday, February 29, 2016  24

------------------------------------------------------------- Window=1 -------------------------------------------------------------

                                                         The GLM Procedure

                                                  Dependent Variable: PSS_2013  

                                                                Sum of

                        Source                      DF         Squares     Mean Square    F Value    Pr > F

                        Model                        1      0.04265381      0.04265381       2.22    0.1387

                        Error                      130      2.49887952      0.01922215                    

                        Corrected Total            131      2.54153333                                    

                                       R-Square     Coeff Var      Root MSE    PSS_2013 Mean

                                       0.016783      64.98936      0.138644         0.213333

                        Source                      DF       Type I SS     Mean Square    F Value    Pr > F

                        H1                           1      0.04265381      0.04265381       2.22    0.1387

                        Source                      DF     Type III SS     Mean Square    F Value    Pr > F

                        H1                           1      0.04265381      0.04265381       2.22    0.1387

                        Contrast                    DF     Contrast SS     Mean Square    F Value    Pr > F

                        H1                           1      0.04265381      0.04265381       2.22    0.1387

                                                                   Standard

                                 Parameter         Estimate           Error    t Value    Pr > |t|

                                 Intercept     0.2058495133      0.01307144      15.75      <.0001

                                 H1            0.0604036959      0.04054951       1.49      0.1387

----------------------------------------------------------------------------------------------------

                                                        Test for Haplotype 2                     16:33 Monday, February 29, 2016  25

------------------------------------------------------------- Window=1 -------------------------------------------------------------

                                                         The GLM Procedure

                                              Number of Observations Read         132

                                              Number of Observations Used         132

----------------------------------------------------------------------------------------------------

                                                        Test for Haplotype 2                     16:33 Monday, February 29, 2016  26

------------------------------------------------------------- Window=1 -------------------------------------------------------------

                                                         The GLM Procedure

                                                  Dependent Variable: PSS_2013  

                                                                Sum of

                        Source                      DF         Squares     Mean Square    F Value    Pr > F

                        Model                        1      0.00464098      0.00464098       0.24    0.6266

                        Error                      130      2.53689236      0.01951456                    

                        Corrected Total            131      2.54153333                                    

                                       R-Square     Coeff Var      Root MSE    PSS_2013 Mean

                                       0.001826      65.48180      0.139695         0.213333

                        Source                      DF       Type I SS     Mean Square    F Value    Pr > F

                        H2                           1      0.00464098      0.00464098       0.24    0.6266

                        Source                      DF     Type III SS     Mean Square    F Value    Pr > F

                        H2                           1      0.00464098      0.00464098       0.24    0.6266

                        Contrast                    DF     Contrast SS     Mean Square    F Value    Pr > F

                        H2                           1      0.00464098      0.00464098       0.24    0.6266

                                                                   Standard

                                 Parameter         Estimate           Error    t Value    Pr > |t|

                                 Intercept     0.2108940059      0.01314754      16.04      <.0001

                                 H2            0.0199012940      0.04080901       0.49      0.6266

----------------------------------------------------------------------------------------------------

                                                        Test for Haplotype 3                     16:33 Monday, February 29, 2016  27

------------------------------------------------------------- Window=1 -------------------------------------------------------------

                                                         The GLM Procedure

                                              Number of Observations Read         132

                                              Number of Observations Used         132

----------------------------------------------------------------------------------------------------

                                                        Test for Haplotype 3                     16:33 Monday, February 29, 2016  28

------------------------------------------------------------- Window=1 -------------------------------------------------------------

                                                         The GLM Procedure

                                                  Dependent Variable: PSS_2013  

                                                                Sum of

                        Source                      DF         Squares     Mean Square    F Value    Pr > F

                        Model                        1      0.18816586      0.18816586      10.39    0.0016

                        Error                      130      2.35336747      0.01810283                    

                        Corrected Total            131      2.54153333                                    

                                       R-Square     Coeff Var      Root MSE    PSS_2013 Mean

                                       0.074036      63.06879      0.134547         0.213333

                        Source                      DF       Type I SS     Mean Square    F Value    Pr > F

                        H3                           1      0.18816586      0.18816586      10.39    0.0016

                        Source                      DF     Type III SS     Mean Square    F Value    Pr > F

                        H3                           1      0.18816586      0.18816586      10.39    0.0016

                        Contrast                    DF     Contrast SS     Mean Square    F Value    Pr > F

                        H3                           1      0.18816586      0.18816586      10.39    0.0016

                                                                   Standard

                                 Parameter         Estimate           Error    t Value    Pr > |t|

                                 Intercept     0.2281706052      0.01258261      18.13      <.0001

                                 H3            -.1357147781      0.04209494      -3.22      0.0016

----------------------------------------------------------------------------------------------------

                                                        Test for Haplotype 4                     16:33 Monday, February 29, 2016  29

------------------------------------------------------------- Window=1 -------------------------------------------------------------

                                                         The GLM Procedure

                                              Number of Observations Read         132

                                              Number of Observations Used         132

----------------------------------------------------------------------------------------------------

                                                        Test for Haplotype 4                     16:33 Monday, February 29, 2016  30

------------------------------------------------------------- Window=1 -------------------------------------------------------------

                                                         The GLM Procedure

                                                  Dependent Variable: PSS_2013  

                                                                Sum of

                        Source                      DF         Squares     Mean Square    F Value    Pr > F

                        Model                        1      0.12443421      0.12443421       6.69    0.0108

                        Error                      130      2.41709913      0.01859307                    

                        Corrected Total            131      2.54153333                                    

                                       R-Square     Coeff Var      Root MSE    PSS_2013 Mean

                                       0.048960      63.91707      0.136356         0.213333

                        Source                      DF       Type I SS     Mean Square    F Value    Pr > F

                        H4                           1      0.12443421      0.12443421       6.69    0.0108

                        Source                      DF     Type III SS     Mean Square    F Value    Pr > F

                        H4                           1      0.12443421      0.12443421       6.69    0.0108

                        Contrast                    DF     Contrast SS     Mean Square    F Value    Pr > F

                        H4                           1      0.12443421      0.12443421       6.69    0.0108

                                                                   Standard

                                 Parameter         Estimate           Error    t Value    Pr > |t|

                                 Intercept     0.2242132838      0.01259143      17.81      <.0001

                                 H4            -.1263698272      0.04884826      -2.59      0.0108

----------------------------------------------------------------------------------------------------

                                                        Test for Haplotype 5                     16:33 Monday, February 29, 2016  31

------------------------------------------------------------- Window=1 -------------------------------------------------------------

                                                         The GLM Procedure

                                              Number of Observations Read         132

                                              Number of Observations Used         132

----------------------------------------------------------------------------------------------------

                                                        Test for Haplotype 5                     16:33 Monday, February 29, 2016  32

------------------------------------------------------------- Window=1 -------------------------------------------------------------

                                                         The GLM Procedure

                                                  Dependent Variable: PSS_2013  

                                                                Sum of

                        Source                      DF         Squares     Mean Square    F Value    Pr > F

                        Model                        1      0.06560886      0.06560886       3.44    0.0657

                        Error                      130      2.47592448      0.01904557                    

                        Corrected Total            131      2.54153333                                    

                                       R-Square     Coeff Var      Root MSE    PSS_2013 Mean

                                       0.025815      64.69017      0.138006         0.213333

                        Source                      DF       Type I SS     Mean Square    F Value    Pr > F

                        H5                           1      0.06560886      0.06560886       3.44    0.0657

                        Source                      DF     Type III SS     Mean Square    F Value    Pr > F

                        H5                           1      0.06560886      0.06560886       3.44    0.0657

                        Contrast                    DF     Contrast SS     Mean Square    F Value    Pr > F

                        H5                           1      0.06560886      0.06560886       3.44    0.0657

                                                                   Standard

                                 Parameter         Estimate           Error    t Value    Pr > |t|

                                 Intercept     0.2208798843      0.01268136      17.42      <.0001

                                 H5            -.0873881772      0.04708347      -1.86      0.0657

----------------------------------------------------------------------------------------------------

                                                        Test for Haplotype 6                     16:33 Monday, February 29, 2016  33

------------------------------------------------------------- Window=1 -------------------------------------------------------------

                                                         The GLM Procedure

                                              Number of Observations Read         132

                                              Number of Observations Used         132

----------------------------------------------------------------------------------------------------

                                                        Test for Haplotype 6                     16:33 Monday, February 29, 2016  34

------------------------------------------------------------- Window=1 -------------------------------------------------------------

                                                         The GLM Procedure

                                                  Dependent Variable: PSS_2013  

                                                                Sum of

                        Source                      DF         Squares     Mean Square    F Value    Pr > F

                        Model                        1      0.00496349      0.00496349       0.25    0.6149

                        Error                      130      2.53656985      0.01951208                    

                        Corrected Total            131      2.54153333                                    

                                       R-Square     Coeff Var      Root MSE    PSS_2013 Mean

                                       0.001953      65.47764      0.139686         0.213333

                        Source                      DF       Type I SS     Mean Square    F Value    Pr > F

                        H6                           1      0.00496349      0.00496349       0.25    0.6149

                        Source                      DF     Type III SS     Mean Square    F Value    Pr > F

                        H6                           1      0.00496349      0.00496349       0.25    0.6149

                        Contrast                    DF     Contrast SS     Mean Square    F Value    Pr > F

                        H6                           1      0.00496349      0.00496349       0.25    0.6149

                                                                   Standard

                                 Parameter         Estimate           Error    t Value    Pr > |t|

                                 Intercept     0.2154476441      0.01286049      16.75      <.0001

                                 H6            -.0252461592      0.05005571      -0.50      0.6149

----------------------------------------------------------------------------------------------------

                                                        Test for Haplotype 7                     16:33 Monday, February 29, 2016  35

------------------------------------------------------------- Window=1 -------------------------------------------------------------

                                                         The GLM Procedure

                                              Number of Observations Read         132

                                              Number of Observations Used         132

----------------------------------------------------------------------------------------------------

                                                        Test for Haplotype 7                     16:33 Monday, February 29, 2016  36

------------------------------------------------------------- Window=1 -------------------------------------------------------------

                                                         The GLM Procedure

                                                  Dependent Variable: PSS_2013  

                                                                Sum of

                        Source                      DF         Squares     Mean Square    F Value    Pr > F

                        Model                        1      0.04871084      0.04871084       2.54    0.1134

                        Error                      130      2.49282249      0.01917556                    

                        Corrected Total            131      2.54153333                                    

                                       R-Square     Coeff Var      Root MSE    PSS_2013 Mean

                                       0.019166      64.91055      0.138476         0.213333

                        Source                      DF       Type I SS     Mean Square    F Value    Pr > F

                        H7                           1      0.04871084      0.04871084       2.54    0.1134

                        Source                      DF     Type III SS     Mean Square    F Value    Pr > F

                        H7                           1      0.04871084      0.04871084       2.54    0.1134

                        Contrast                    DF     Contrast SS     Mean Square    F Value    Pr > F

                        H7                           1      0.04871084      0.04871084       2.54    0.1134

                                                                   Standard

                                 Parameter         Estimate           Error    t Value    Pr > |t|

                                 Intercept     0.2071830763      0.01265543      16.37      <.0001

                                 H7            0.0721643793      0.04527767       1.59      0.1134

----------------------------------------------------------------------------------------------------

                                                        Test for Haplotype 8                     16:33 Monday, February 29, 2016  37

------------------------------------------------------------- Window=1 -------------------------------------------------------------

                                                         The GLM Procedure

                                              Number of Observations Read         132

                                              Number of Observations Used         132

----------------------------------------------------------------------------------------------------

                                                        Test for Haplotype 8                     16:33 Monday, February 29, 2016  38

------------------------------------------------------------- Window=1 -------------------------------------------------------------

                                                         The GLM Procedure

                                                  Dependent Variable: PSS_2013  

                                                                Sum of

                        Source                      DF         Squares     Mean Square    F Value    Pr > F

                        Model                        1      0.52691021      0.52691021      34.00    <.0001

                        Error                      130      2.01462312      0.01549710                    

                        Corrected Total            131      2.54153333                                    

                                       R-Square     Coeff Var      Root MSE    PSS_2013 Mean

                                       0.207320      58.35345      0.124487         0.213333

                        Source                      DF       Type I SS     Mean Square    F Value    Pr > F

                        H8                           1      0.52691021      0.52691021      34.00    <.0001

                        Source                      DF     Type III SS     Mean Square    F Value    Pr > F

                        H8                           1      0.52691021      0.52691021      34.00    <.0001

                        Contrast                    DF     Contrast SS     Mean Square    F Value    Pr > F

                        H8                           1      0.52691021      0.52691021      34.00    <.0001

                                                                   Standard

                                 Parameter         Estimate           Error    t Value    Pr > |t|

                                 Intercept     0.1932524844      0.01136935      17.00      <.0001

                                 H8            0.2484527632      0.04260894       5.83      <.0001

====================================================================================================

1 ACCEPTED SOLUTION

Accepted Solutions
Solution

Hi,

If I understood your question correctly, you want the Least Square Means (LS Means) of each haplotype. Since you have results from the Overall Test and Individual Test, you can get two LS Means estimates for each haplotype. In either case, the LS Means for the haplotype is the sum of the Intercept and the haplotype estimate. The LS Means from the Overall Test is conditional on other haplotypes fitted together in the model and it may change if you change the model (say, remove haplotypes from the model), while the LS Means from the Individual Test is unconditional to other haplotypes because the model has only one haplotype.

 

LS Means H1 (overall test) = 0.2890451760 + (-.0302601288) = 0.2587850472

LS Means H1 (individual test) = 0.2058495133 + 0.0604036959 = 0.2662532092

Sincerely yours,

Luciano Silva 

3 REPLIES
chris_kirchberg

Joined:

May 28, 2014

Hi,

Thanks for posting this question.

First, if you are looking for the mean for your trait (PSS_2013) for each haplotype, then take a look at each section labelled Test for Haplotype Hx where x is the Haplotype number. Within each section there is an item called PSS_2013 Mean. That would be the mean for the trait for that haplotype. Is that what you are looking for? These individual sections for each haplotype are the individual tests for each haplotype as opposed to the whole model fit where all haplotypes are fit together (at the beginning) and the PSS_2013 Mean is the mean for the whole fit, instead of the individual fits.

The Parameter Estimates are the slope of the fit for each haplotype as individual tests or the whole model fit and represent the effect (+ is a positive effect and - is a negative effect) on that trait for each haplotype or when fit together, their effect when considering the other haplotypes.

Does that help explain the output?

Best,

Chris Kirchberg

Solution

Hi,

If I understood your question correctly, you want the Least Square Means (LS Means) of each haplotype. Since you have results from the Overall Test and Individual Test, you can get two LS Means estimates for each haplotype. In either case, the LS Means for the haplotype is the sum of the Intercept and the haplotype estimate. The LS Means from the Overall Test is conditional on other haplotypes fitted together in the model and it may change if you change the model (say, remove haplotypes from the model), while the LS Means from the Individual Test is unconditional to other haplotypes because the model has only one haplotype.

 

LS Means H1 (overall test) = 0.2890451760 + (-.0302601288) = 0.2587850472

LS Means H1 (individual test) = 0.2058495133 + 0.0604036959 = 0.2662532092

Sincerely yours,

Luciano Silva 

sbrlsi

Staff

Joined:

Jun 20, 2014

Hi,

I must correct myself when I said LS Means in the previous reply; instead, the values I defined as LS Means are indeed the predicted means for each haplotype.

My apologies.

Luciano Silva