Contrast matrix for a continuous covariate - for EGSEA algorithm
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@stefanomangiola-6873
Last seen 3 months ago
Australia

Hello,

 

I have a simple design matrix as such

 

                                                                      (Intercept) CAPRA_TOTAL
merged_100HQ.N728.S517_S32_trimmedBBduk.Aligned.out.sam           1           4
merged_300.N728.S516_S52_trimmedBBduk.Aligned.out.sam             1           7
merged_100HQ.N721.S516_S18_trimmedBBduk.Aligned.out.sam           1           2
merged_100HQ.N728.S506_S29_trimmedBBduk.Aligned.out.sam           1           1
merged_100HQ.N721.S513_S16_trimmedBBduk.Aligned.out.sam           1           1
merged_100HQ.N721.S502_S13_trimmedBBduk.Aligned.out.sam           1           3
merged_100HQ.N721.S503_S14_trimmedBBduk.Aligned.out.sam           1           6
merged_100HQ.N728.S515_S31_trimmedBBduk.Aligned.out.sam           1           3
merged_100HQ.N728.S503_S28_trimmedBBduk.Aligned.out.sam           1           0
merged_100HQ.N721.S515_S17_trimmedBBduk.Aligned.out.sam           1           3
merged_100HQ.N728.S502_S27_trimmedBBduk.Aligned.out.sam           1           1
merged_100HQ.N728.S513_S30_trimmedBBduk.Aligned.out.sam           1           0
merged_100HQ.N721.S506_S15_trimmedBBduk.Aligned.out.sam           1           0

 

With CAPRA_TOTAL being a continuous rounded disease risk score. The algorithm EGSEA requests a contrast matrix, however it is not clear to me how it can be implemented for a continuous covariate.

 

Thanks a lot.

design and contrast matrix egsea • 362 views
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