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library(lmerTest)
map <- read.table("/mnt/ultrastarQuatre/Microbiome/Skin/skin_pool/skin1234567/No_Ear_Face/Alpha_Diversity_11766_Depth/final_map.txt", sep = '\t', header=TRUE)
choa1_file <- read.table("/mnt/ultrastarQuatre/Microbiome/Skin/skin_pool/skin1234567/No_Ear_Face/Alpha_Diversity_11766_Depth/chao1.txt", sep = '\t', header =TRUE)
simpson_file <- read.table("/mnt/ultrastarQuatre/Microbiome/Skin/skin_pool/skin1234567/No_Ear_Face/Alpha_Diversity_11766_Depth/simpson.txt", sep = '\t', header =TRUE)merge the two tables
mdata <- merge(map,choa1_file,by="SampleID")
mdata <- merge(mdata,simpson_file, by="SampleID")
mdata <- mdata[,c(1,5,9,10,13,14)]
mdata <- merge(mdata, beta_file, by="SampleID")LME with Healthy as reference
mdata$Treatment <- factor(mdata$Treatment,levels=c("Healthy","PSO_L","PSO_N"))
### Chao1 stats (reference=Healthy)
chao1.model.healthy = lmer(Chao1 ~ Treatment + (1|Patient) , data=mdata)
summary(chao1.model.healthy)Linear mixed model fit by REML
t-tests use Satterthwaite approximations to degrees of freedom ['lmerMod']
Formula: Chao1 ~ Treatment + (1 | Patient)
Data: mdata
REML criterion at convergence: 6441.2
Scaled residuals:
Min 1Q Median 3Q Max
-2.3497 -0.5633 -0.0451 0.4410 4.3364
Random effects:
Groups Name Variance Std.Dev.
Patient (Intercept) 102521 320.2
Residual 272936 522.4
Number of obs: 417, groups: Patient, 54
Fixed effects:
Estimate Std. Error df t value Pr(>|t|)
(Intercept) 888.58 76.24 63.58 11.654 <2e-16 ***
TreatmentPSO_L 168.07 109.55 72.24 1.534 0.129
TreatmentPSO_N 124.73 105.90 63.64 1.178 0.243
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Correlation of Fixed Effects:
(Intr) TPSO_L
TrtmntPSO_L -0.696
TrtmntPSO_N -0.720 0.817### Simpson stats (reference= Healthy)
simpson.model.healthy = lmer(Simpson ~Treatment +(1|Patient), data=mdata)
summary(simpson.model.healthy)Linear mixed model fit by REML
t-tests use Satterthwaite approximations to degrees of freedom ['lmerMod']
Formula: Simpson ~ Treatment + (1 | Patient)
Data: mdata
REML criterion at convergence: -265.2
Scaled residuals:
Min 1Q Median 3Q Max
-4.1327 -0.3715 0.2769 0.5856 1.8460
Random effects:
Groups Name Variance Std.Dev.
Patient (Intercept) 0.00963 0.09813
Residual 0.02513 0.15852
Number of obs: 417, groups: Patient, 54
Fixed effects:
Estimate Std. Error df t value Pr(>|t|)
(Intercept) 0.77381 0.02329 59.82000 33.222 <2e-16 ***
TreatmentPSO_L 0.05284 0.03345 67.95000 1.579 0.119
TreatmentPSO_N 0.03621 0.03235 59.87000 1.119 0.268
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Correlation of Fixed Effects:
(Intr) TPSO_L
TrtmntPSO_L -0.696
TrtmntPSO_N -0.720 0.819### Beta-diversity (PC1) stats (reference= Healthy)
beta.pc1.healthy = lmer(PC1 ~ Treatment + (1|Patient), data = mdata)
summary(beta.pc1.healthy)Linear mixed model fit by REML
t-tests use Satterthwaite approximations to degrees of freedom ['lmerMod']
Formula: PC1 ~ Treatment + (1 | Patient)
Data: mdata
REML criterion at convergence: -348.4
Scaled residuals:
Min 1Q Median 3Q Max
-2.54785 -0.62132 -0.03505 0.67839 2.97771
Random effects:
Groups Name Variance Std.Dev.
Patient (Intercept) 0.008044 0.08969
Residual 0.020505 0.14319
Number of obs: 417, groups: Patient, 54
Fixed effects:
Estimate Std. Error df t value Pr(>|t|)
(Intercept) 0.03222 0.02121 61.44000 1.519 0.134
TreatmentPSO_L -0.04946 0.03045 69.63000 -1.624 0.109
TreatmentPSO_N -0.04547 0.02946 61.49000 -1.543 0.128
Correlation of Fixed Effects:
(Intr) TPSO_L
TrtmntPSO_L -0.697
TrtmntPSO_N -0.720 0.822RME using PSO_N as reference
mdata$Treatment <- factor(mdata$Treatment,levels=c("PSO_N","PSO_L","Healthy"))
### Chao1 stats (refence = PSO_N)
chao1.model.PSO_N = lmer(Chao1 ~ Treatment + (1|Patient) , data=mdata)
summary(chao1.model.PSO_N)Linear mixed model fit by REML
t-tests use Satterthwaite approximations to degrees of freedom ['lmerMod']
Formula: Chao1 ~ Treatment + (1 | Patient)
Data: mdata
REML criterion at convergence: 6441.2
Scaled residuals:
Min 1Q Median 3Q Max
-2.3497 -0.5633 -0.0451 0.4410 4.3364
Random effects:
Groups Name Variance Std.Dev.
Patient (Intercept) 102521 320.2
Residual 272936 522.4
Number of obs: 417, groups: Patient, 54
Fixed effects:
Estimate Std. Error df t value Pr(>|t|)
(Intercept) 1013.31 73.49 63.70 13.788 <2e-16 ***
TreatmentPSO_L 43.34 65.30 372.20 0.664 0.507
TreatmentHealthy -124.73 105.90 63.60 -1.178 0.243
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Correlation of Fixed Effects:
(Intr) TPSO_L
TrtmntPSO_L -0.362
TrtmntHlthy -0.694 0.251### Simpson stats (reference= PSO_N)
simpson.model.PSO_N = lmer(Simpson ~Treatment +(1|Patient), data=mdata)
summary(simpson.model.PSO_N)Linear mixed model fit by REML
t-tests use Satterthwaite approximations to degrees of freedom ['lmerMod']
Formula: Simpson ~ Treatment + (1 | Patient)
Data: mdata
REML criterion at convergence: -265.2
Scaled residuals:
Min 1Q Median 3Q Max
-4.1327 -0.3715 0.2769 0.5856 1.8460
Random effects:
Groups Name Variance Std.Dev.
Patient (Intercept) 0.00963 0.09813
Residual 0.02513 0.15852
Number of obs: 417, groups: Patient, 54
Fixed effects:
Estimate Std. Error df t value Pr(>|t|)
(Intercept) 0.81002 0.02245 59.90000 36.078 <2e-16 ***
TreatmentPSO_L 0.01663 0.01981 367.50000 0.839 0.402
TreatmentHealthy -0.03621 0.03235 59.90000 -1.119 0.268
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Correlation of Fixed Effects:
(Intr) TPSO_L
TrtmntPSO_L -0.360
TrtmntHlthy -0.694 0.250### Beta-diversity (PC1) stats (reference= PSO_N)
beta.pc1.PSO_N = lmer(PC1 ~ Treatment + (1|Patient), data = mdata)
summary(beta.pc1.PSO_N)Linear mixed model fit by REML
t-tests use Satterthwaite approximations to degrees of freedom ['lmerMod']
Formula: PC1 ~ Treatment + (1 | Patient)
Data: mdata
REML criterion at convergence: -348.4
Scaled residuals:
Min 1Q Median 3Q Max
-2.54785 -0.62132 -0.03505 0.67839 2.97771
Random effects:
Groups Name Variance Std.Dev.
Patient (Intercept) 0.008044 0.08969
Residual 0.020505 0.14319
Number of obs: 417, groups: Patient, 54
Fixed effects:
Estimate Std. Error df t value Pr(>|t|)
(Intercept) -0.013249 0.020445 61.600000 -0.648 0.519
TreatmentPSO_L -0.003989 0.017900 368.800000 -0.223 0.824
TreatmentHealthy 0.045469 0.029460 61.500000 1.543 0.128
Correlation of Fixed Effects:
(Intr) TPSO_L
TrtmntPSO_L -0.357
TrtmntHlthy -0.694 0.248