Combined Compounds

Section

Other anlayses

Weight trajectory

Definitely different

## `geom_smooth()` using formula = 'y ~ s(x, bs = "cs")'
## `geom_smooth()` using formula = 'y ~ s(x, bs = "cs")'

## Loading required package: nlme
## 
## Attaching package: 'nlme'
## 
## The following object is masked from 'package:IRanges':
## 
##     collapse
## 
## The following object is masked from 'package:dplyr':
## 
##     collapse
## 
## The following object is masked from 'package:lme4':
## 
##     lmList
## 
## This is mgcv 1.9-1. For overview type 'help("mgcv-package")'.

Sex	Genotype	p
Males	Tp53	1.18e-05
Females	Tp53	0.00e+00
Males	WT	3.00e-07
Females	WT	0.00e+00

Lean Trajectory

Belive it or not, a little different

Sex	Genotype	p
Males	Tp53	0.0138988
Females	Tp53	0.0004708
Males	WT	0.0032615
Females	WT	0.0000000

Fat Trajectory

Very different

Sex	Genotype	p
Males	Tp53	0
Females	Tp53	0
Males	WT	0
Females	WT	0

Prevalence

We want to know if prevalence of cancer differs between HFD and NC. Not enough evidence of a difference and not enough evidence to establish equivalence.

Female: diet differenc by Genotypes

contrast	genotype	estimate	SE	df	z.ratio	p.value
HFD - NC	Tp53	0.0640029	0.5883106	Inf	0.1087910	0.9133683
HFD - NC	WT	-1.6094379	2.1447611	Inf	-0.7504043	0.4530112

Female: Genotype difference by diet

contrast	diet	estimate	SE	df	z.ratio	p.value
Tp53 - WT	HFD	1.2602536	1.066926	Inf	1.1812007	0.2375230
Tp53 - WT	NC	-0.4131872	1.951353	Inf	-0.2117439	0.8323068

##                        2.5 %    97.5 %
## (Intercept)        0.5312869 1.9892203
## dietNC            -1.2170704 1.0890647
## genotypeWT        -3.3513900 0.8308827
## dietNC:genotypeWT -2.6854897 6.0323713

Male: diet differenc by Genotypes

contrast	genotype	estimate	SE	df	z.ratio	p.value
HFD - NC	Tp53	0.4161604	0.7592179	Inf	0.5481436	0.5835933
HFD - NC	WT	0.2513144	1.2445011	Inf	0.2019399	0.8399637

Male: Genotype difference by diet

contrast	diet	estimate	SE	df	z.ratio	p.value
Tp53 - WT	HFD	1.0651364	1.000254	Inf	1.064866	0.2869366
Tp53 - WT	NC	0.9002904	1.060513	Inf	0.848920	0.3959258

##                        2.5 %    97.5 %
## (Intercept)        0.6258908 2.6799552
## dietNC            -1.9042001 1.0718793
## genotypeWT        -3.0255980 0.8953252
## dietNC:genotypeWT -2.6923989 3.0220909

##                        2.5 %    97.5 %
## (Intercept)        0.8335106 2.0295913
## dietNC            -1.1015791 0.7303512
## genotypeWT        -2.4590927 0.3314403
## dietNC:genotypeWT -1.6257890 2.8384821

Burden

Not enough evidence of a difference and not enough evidence to establish equivalence.

Female: diet differences

contrast	genotype	estimate	SE	df	t.ratio	p.value
HFD - NC	Tp53	7.76455	4.493877	71	1.7278066	0.0883704
HFD - NC	WT	11.12500	15.777340	71	0.7051252	0.4830392

Female: genotype differences

contrast	diet	estimate	SE	df	t.ratio	p.value
Tp53 - WT	HFD	5.398809	9.532953	71	0.5663313	0.5729544
Tp53 - WT	NC	8.759259	13.350738	71	0.6560880	0.5138881

##                       2.5 %    97.5 %
## (Intercept)        35.91861 47.129012
## genotypeWT        -24.40698 13.609358
## dietNC            -16.72509  1.195986
## genotypeWT:dietNC -36.07081 29.349910

Male: diet differences

contrast	genotype	estimate	SE	df	t.ratio	p.value
HFD - NC	Tp53	3.558479	4.668739	53	0.7621928	0.4493237
HFD - NC	WT	-2.483333	9.440937	53	-0.2630389	0.7935405

Male: genotype differences

contrast	diet	estimate	SE	df	t.ratio	p.value
Tp53 - WT	HFD	13.694444	7.036859	53	1.9461019	0.0569529
Tp53 - WT	NC	7.652632	7.836519	53	0.9765346	0.3332360

##                       2.5 %     97.5 %
## (Intercept)        26.59282 38.6294055
## genotypeWT        -27.80860  0.4197069
## dietNC            -12.92278  5.8058252
## genotypeWT:dietNC -15.08322 27.1668427

Malignancy

Female: diet differenc by Genotypes

contrast	genotype	estimate	SE	df	z.ratio	p.value
HFD - NC	Tp53	0.00000	0.309461	Inf	0.000000	1.0000000
HFD - NC	WT	1.94591	1.927248	Inf	1.009683	0.3126471

Female: Genotype difference by diet

contrast	diet	estimate	SE	df	z.ratio	p.value
Tp53 - WT	HFD	-1.94591	1.7546704	Inf	-1.108989	0.267435
Tp53 - WT	NC	0.00000	0.8550923	Inf	0.000000	1.000000

##                        2.5 %    97.5 %
## (Intercept)       -0.3464760 0.3464760
## dietNC            -0.6065325 0.6065325
## genotypeWT        -1.4931810 5.3850005
## dietNC:genotypeWT -5.7716324 1.8798129

Male: diet differenc by Genotypes

contrast	genotype	estimate	SE	df	z.ratio	p.value
HFD - NC	Tp53	0	0.3382603	Inf	0	1
HFD - NC	WT	0	0.7559289	Inf	0	1

Male: Genotype difference by diet

contrast	diet	estimate	SE	df	z.ratio	p.value
Tp53 - WT	HFD	0	0.5754727	Inf	0	1
Tp53 - WT	NC	0	0.5955500	Inf	0	1

##                        2.5 %    97.5 %
## (Intercept)       -0.4178657 0.4178657
## dietNC            -0.6629781 0.6629781
## genotypeWT        -1.1279058 1.1279058
## dietNC:genotypeWT -1.6231634 1.6231634

Survival

No Diet differences and not enough evidence of equivalence

## Loading required package: ggpubr

## 
## Attaching package: 'survminer'

## The following object is masked from 'package:survival':
## 
##     myeloma

## Call:
## coxph(formula = Surv(time = age_sacrifice, event = status) ~ 
##     diet + sex, data = surv[surv$genotype == "Tp53", ])
## 
##   n= 173, number of events= 92 
## 
##            coef exp(coef) se(coef)      z Pr(>|z|)
## dietNC -0.02173   0.97850  0.21388 -0.102    0.919
## sexM   -0.15480   0.85659  0.21204 -0.730    0.465
## 
##        exp(coef) exp(-coef) lower .95 upper .95
## dietNC    0.9785      1.022    0.6434     1.488
## sexM      0.8566      1.167    0.5653     1.298
## 
## Concordance= 0.497  (se = 0.031 )
## Likelihood ratio test= 0.55  on 2 df,   p=0.8
## Wald test            = 0.54  on 2 df,   p=0.8
## Score (logrank) test = 0.54  on 2 df,   p=0.8

## Call:
## coxph(formula = Surv(time = age_sacrifice, event = status) ~ 
##     diet, data = surv[surv$genotype == "WT" & surv$sex == "M", 
##     ])
## 
##   n= 23, number of events= 7 
## 
##          coef exp(coef) se(coef)     z Pr(>|z|)
## dietNC 0.3346    1.3974   0.7652 0.437    0.662
## 
##        exp(coef) exp(-coef) lower .95 upper .95
## dietNC     1.397     0.7156    0.3119     6.261
## 
## Concordance= 0.573  (se = 0.101 )
## Likelihood ratio test= 0.19  on 1 df,   p=0.7
## Wald test            = 0.19  on 1 df,   p=0.7
## Score (logrank) test = 0.19  on 1 df,   p=0.7

## New names:
## New names:
## • `weight_14w` -> `weight_14w...58`
## • `weight_54w` -> `weight_54w...91`
## • `weight_56w` -> `weight_56w...92`
## • `weight_58w` -> `weight_58w...93`
## • `weight_62w` -> `weight_62w...97`
## • `weight_64w` -> `weight_64w...98`
## • `weight_66w` -> `weight_66w...99`
## • `weight_68w` -> `weight_68w...100`
## • `weight_14w` -> `weight_14w...136`
## • `weight_54w` -> `weight_54w...187`
## • `weight_56w` -> `weight_56w...193`
## • `weight_58w` -> `weight_58w...199`
## • `weight_62w` -> `weight_62w...208`
## • `weight_64w` -> `weight_64w...214`
## • `weight_66w` -> `weight_66w...220`
## • `weight_68w` -> `weight_68w...226`

Compounds

Missingness

Males

Females

Survival corrs

Pooled: Compounds with evidence of Survival impact

Compund	coef	exp.coef.	se.coef.	z	Pr…z..	FDR	Lower	Upper	sgpv
C30pos:638.5717@17.3	-0.4838477	0.6164071	0.1729910	-2.796953	0.0051587	0.9992651	-0.8229102	-0.1447853	0
T3pos:194.1176@3.7	-0.2957942	0.7439405	0.0936713	-3.157790	0.0015897	0.9992651	-0.4793900	-0.1121985	0
T3pos:256.2636@12.29	-0.4247455	0.6539362	0.1507079	-2.818336	0.0048273	0.9992651	-0.7201330	-0.1293581	0
T3pos:327.2016@4.84	-0.7561469	0.4694719	0.2489805	-3.036973	0.0023897	0.9992651	-1.2441486	-0.2681452	0
T3pos:252.9729@0.14	-0.4965025	0.6086557	0.1498272	-3.313834	0.0009203	0.9992651	-0.7901637	-0.2028412	0

## `geom_smooth()` using formula = 'y ~ x'

Males: Compounds with evidence of Survival impact

Compund	coef	exp.coef.	se.coef.	z	Pr…z..	FDR	Lower	Upper	sgpv
C18neg:817.6443@15.42	-0.3916688	0.6759279	0.1135916	-3.448043	0.0005647	0.9064277	-0.6143084	-0.1690292	0
C18neg:698.32@4.49	0.3821763	1.4654704	0.1188226	3.216361	0.0012983	0.9064277	0.1492841	0.6150685	0
C30pos:504.3238@2.14	1.1434454	3.1375600	0.5195804	2.200709	0.0277566	0.9064277	0.1250678	2.1618230	0
C30pos:750.543@13.54	-0.7952090	0.4514868	0.2304766	-3.450281	0.0005600	0.9064277	-1.2469432	-0.3434749	0
C30pos:703.5744@11.73	-0.8491183	0.4277920	0.3190392	-2.661486	0.0077797	0.9064277	-1.4744351	-0.2238014	0
C30pos:688.6024@22.78	-0.5263273	0.5907707	0.1992225	-2.641906	0.0082441	0.9064277	-0.9168034	-0.1358511	0
C30pos:974.8167@22.25	-0.4712506	0.6242212	0.1513247	-3.114168	0.0018446	0.9064277	-0.7678470	-0.1746541	0
C30pos:949.7251@21.64	-0.4593693	0.6316819	0.1653925	-2.777449	0.0054787	0.9064277	-0.7835387	-0.1352000	0
C30pos:943.7148@22.2	-0.4264444	0.6528262	0.1478559	-2.884190	0.0039242	0.9064277	-0.7162419	-0.1366469	0
C30pos:934.8795@24.76	-0.2856603	0.7515179	0.0847733	-3.369697	0.0007525	0.9064277	-0.4518159	-0.1195046	0
C30pos:770.5688@15.38	0.5924928	1.8084909	0.2492729	2.376884	0.0174596	0.9064277	0.1039178	1.0810677	0
C30pos:354.285@1.29	0.4075811	1.5031773	0.1569389	2.597069	0.0094023	0.9064277	0.0999809	0.7151812	0
C30pos:952.8325@21.56	0.3017546	1.3522293	0.1041577	2.897092	0.0037664	0.9064277	0.0976054	0.5059037	0
PHneg:431.1839@9.54	0.3386821	1.4030973	0.1103918	3.068002	0.0021550	0.9064277	0.1223143	0.5550500	0
PHneg:291.0738@5.54	0.4688826	1.5982074	0.1483278	3.161125	0.0015716	0.9064277	0.1781602	0.7596050	0
T3pos:223.0637@1.11	-0.4246275	0.6540134	0.1594045	-2.663837	0.0077255	0.9064277	-0.7370603	-0.1121947	0
T3pos:256.2636@12.29	-0.4346755	0.6474747	0.1636587	-2.655988	0.0079077	0.9064277	-0.7554466	-0.1139044	0
T3pos:194.1082@4.49	-0.4398274	0.6441476	0.1599617	-2.749579	0.0059672	0.9064277	-0.7533524	-0.1263024	0
T3pos:167.5485@0.93	-0.4678968	0.6263182	0.1784110	-2.622579	0.0087267	0.9064277	-0.8175823	-0.1182113	0
T3pos:327.2016@4.84	-0.7642262	0.4656942	0.3100673	-2.464710	0.0137124	0.9064277	-1.3719582	-0.1564942	0
T3pos:118.1227@3.62	-0.5762843	0.5619827	0.2206905	-2.611278	0.0090205	0.9064277	-1.0088377	-0.1437308	0

Females: Compounds with evidence of Survival impact

Compund	coef	exp.coef.	se.coef.	z	Pr…z..	FDR	Lower	Upper	sgpv
C18neg:590.3464@2.81	-0.7872114	4.551122e-01	0.2764460	-2.847613	0.0044048	0.8298124	-1.3290456	-0.2453771	0
C18neg:916.5379@11.0	0.4179887	1.518904e+00	0.1573613	2.656237	0.0079018	0.8298124	0.1095607	0.7264168	0
C18neg:834.566@10.81	0.3976324	1.488297e+00	0.1422653	2.795007	0.0051899	0.8298124	0.1187924	0.6764724	0
C18neg:898.5606@8.44	0.4076786	1.503324e+00	0.1569418	2.597642	0.0093866	0.8298124	0.1000727	0.7152844	0
C30pos:758.5686@12.53	-0.5739910	5.632729e-01	0.2296501	-2.499415	0.0124398	0.8298124	-1.0241053	-0.1238768	0
C30pos:890.8169@23.14	-0.6692993	5.120673e-01	0.2683050	-2.494547	0.0126118	0.8298124	-1.1951770	-0.1434215	0
C30pos:854.6378@14.38	1.2309357	3.424432e+00	0.5506128	2.235574	0.0253797	0.8298124	0.1517345	2.3101369	0
C30pos:766.6918@21.69	0.7152617	2.044722e+00	0.3091365	2.313741	0.0206819	0.8298124	0.1093543	1.3211692	0
C30pos:712.603@22.58	0.2951851	1.343375e+00	0.0834102	3.538959	0.0004017	0.8298124	0.1317012	0.4586690	0
C30pos:511.283@5.76	-0.3279674	7.203865e-01	0.1099157	-2.983810	0.0028468	0.8298124	-0.5434021	-0.1125327	0
C30pos:819.632@20.77	-0.9048658	4.045962e-01	0.3426837	-2.640528	0.0082777	0.8298124	-1.5765259	-0.2332057	0
C30pos:898.7855@22.65	0.3375829	1.401556e+00	0.1052583	3.207185	0.0013404	0.8298124	0.1312766	0.5438892	0
C30pos:894.8845@24.25	-0.3576799	6.992969e-01	0.1048384	-3.411726	0.0006455	0.8298124	-0.5631631	-0.1521966	0
C30pos:916.7082@20.48	-0.3807137	6.833735e-01	0.1370067	-2.778797	0.0054561	0.8298124	-0.6492468	-0.1121806	0
PHneg:191.0198@3.63	-0.5598646	5.712864e-01	0.2127538	-2.631514	0.0085005	0.8298124	-0.9768621	-0.1428671	0
PHneg:286.0602@1.36	0.7266062	2.068050e+00	0.2954054	2.459691	0.0139057	0.8298124	0.1476115	1.3056009	0
PHneg:343.9949@4.27	-0.4606992	6.308424e-01	0.1731253	-2.661074	0.0077892	0.8298124	-0.8000249	-0.1213736	0
PHneg:106.0047@12.58	11.9188422	1.500678e+05	5.7629936	2.068169	0.0386242	0.8298124	0.6233747	23.2143097	0
T3pos:160.0757@3.89	0.3713545	1.449697e+00	0.1254828	2.959405	0.0030823	0.8298124	0.1254082	0.6173008	0
T3pos:148.0427@1.98	-0.5728418	5.639206e-01	0.1975014	-2.900444	0.0037263	0.8298124	-0.9599446	-0.1857391	0

Burden Corrs

Compounds with evidence of burden impact

Compund	Estimate	Std..Error	t.value	Pr…t..	FDR	Lower	Upper	sgpv

limma

## 
## Attaching package: 'limma'

## The following object is masked from 'package:BiocGenerics':
## 
##     plotMA

8 Weeks

Males

Females

Pooled

16 Weeks

Males

Females

Pooled

40 Weeks

Males

Females

Pooled