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Knit directory: Immunue_Cell_Study/
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confounder=read.csv("//dartfs-hpc.dartmouth.edu/rc/lab/M/MRKepistor7/collab/JieZhou/SourceFiles/req19jul2019_ym_06jul2020.csv")
linkage=read.csv("//dartfs-hpc.dartmouth.edu/rc/lab/M/MRKepistor7/collab/JieZhou/SourceFiles/MBLID_linkage.csv")colnames(data6w)[1:2]=c("subject","time")
colnames(data12m)[1:2]=c("subject","time")
name6w=colnames(data6w)[-c(1,2)]
name12m=colnames(data12m)[-c(1,2)]
jointname=unique(c(name6w, name12m))
n1=nrow(data6w)
n2=nrow(data12m)
data6w_swell=data.frame(matrix(nrow = n1,ncol = length(jointname)))
data12m_swell=data.frame(matrix(nrow = n2,ncol = length(jointname)))
for (j in 1:length(jointname)) {
index1=which(name6w==jointname[j])
index2=which(name12m==jointname[j])
if (length(index1)==1){
data6w_swell[,j]=data6w[,index1+2]
}else{
data6w_swell[,j]=0
}
if (length(index2)==1){
data12m_swell[,j]=data12m[,index2+2]
}else{
data12m_swell[,j]=0
}
}
data6w_swell=cbind(data6w$subject,data6w$time, data6w_swell)
rownames(data6w_swell)=rownames(data6w)
colnames(data6w_swell)=c("subject","time",jointname)
data12m_swell=cbind(data12m$subject,data12m$time, data12m_swell)
rownames(data12m_swell)=rownames(data12m)
colnames(data12m_swell)=c("subject","time",jointname)
data6w12m=rbind(data6w_swell,data12m_swell)
#which(apply(data6w12m[,-c(1,2)], 2, sum)==0)
data6w12m=data6w12m[,-207]
index=order(data6w12m$subject,data6w12m$time)
data6w12m=data6w12m[index,]
save(data6w12m,file = "data6w12m.Rdata")overlap=intersect(data6w_swell$subject,data12m_swell$subject)
##overlapping data
data12msub=data.frame()
df.bcelladj_o=data.frame()
df.cd4tadj_o=data.frame()
df.cd8tadj_o=data.frame()
df.cd8tcd4tadj_o=data.frame()
df.monoadj_o=data.frame()
df.nkadj_o=data.frame()
df.nrbcadj_o=data.frame()
df.granadj_o=data.frame()
for (i in 1:length(overlap)) {
index1=which(data12m_swell$subject==overlap[i])
a=data12m_swell[index1,]
data12msub=rbind(data12msub,a)
index1=which(df.bcelladj6w$subject6w==overlap[i])
a=df.bcelladj6w[index1,]
df.bcelladj_o=rbind(df.bcelladj_o,a)
a=df.cd4tadj6w[index1,]
df.cd4tadj_o=rbind(df.cd4tadj_o,a)
a=df.cd8tadj6w[index1,]
df.cd8tadj_o=rbind(df.cd8tadj_o,a)
a=df.cd8tcd4tadj6w[index1,]
df.cd8tcd4tadj_o=rbind(df.cd8tcd4tadj_o,a)
a=df.monoadj6w[index1,]
df.monoadj_o=rbind(df.monoadj_o,a)
a=df.nkadj6w[index1,]
df.nkadj_o=rbind(df.nkadj_o,a)
a=df.nrbcadj6w[index1,]
df.nrbcadj_o=rbind(df.nrbcadj_o,a)
a=df.granadj6w[index1,]
df.granadj_o=rbind(df.granadj_o,a)
}
longidata=rbind(data6w_swell,data12msub)
longibcell=rbind(df.bcelladj6w,df.bcelladj_o)
longicd4=rbind(df.cd4tadj6w,df.cd4tadj_o)
longicd8=rbind(df.cd8tadj6w, df.cd8tadj_o)
longicd8cd4=rbind(df.cd8tcd4tadj6w,df.cd8tcd4tadj_o)
longimono=rbind(df.monoadj6w,df.monoadj_o)
longink=rbind(df.nkadj6w,df.nkadj_o)
longinrbc=rbind(df.nrbcadj6w,df.nrbcadj_o)
longigran=rbind(df.granadj6w,df.granadj_o)library(vegan)Warning: package 'vegan' was built under R version 4.1.3Loading required package: permuteWarning: package 'permute' was built under R version 4.1.3Loading required package: latticeThis is vegan 2.6-2index=order(longidata[,1],longidata[,2])
longidata=longidata[index,]
alpha6w=diversity(data6w_swell[,-c(1,2)],index = "shannon")
alpha12m=diversity(data12msub[,-c(1,2)],index = "shannon")
alpha=diversity(longidata[,-c(1,2)],index = "shannon")
longibcell=cbind(longibcell[index,],alpha)
longicd4=cbind(longicd4[index,],alpha)
longicd8=cbind(longicd8[index,],alpha)
longicd8cd4=cbind(longicd8cd4[index,],alpha)
longigran=cbind(longigran[index,],alpha)
longimono=cbind(longimono[index,],alpha)
longink=cbind(longink[index,],alpha)
longinrbc=cbind(longinrbc[index,],alpha)exmblid=rownames(longidata)
deliver=c()
for (i in 1:length(exmblid)) {
index2=which(linkage[,2]==exmblid[i])
unq_id=linkage[index2,1]
index3=which(confounder[,1]==unq_id)
a=confounder$deliverytype[index3]
deliver=c(deliver,a)
}longibcell=cbind(longibcell,deliver)
longicd4=cbind(longicd4,deliver)
longicd8=cbind(longicd8,deliver)
longimono=cbind(longimono,deliver)
longink=cbind(longink,deliver)
longinrbc=cbind(longinrbc,deliver)
longigran=cbind(longigran,deliver)ss=df.granadj6w$subject6w
dd=c()
for (i in 1:73) {
index=which(longibcell$subject6w==ss[i])[1]
dd=c(dd,longibcell$deliver[index])
}options(warn = 2)
m=ncol(longidata)-2
n=nrow(longidata)
name=colnames(longidata)[-c(1,2)]
microbe=c()
rrbcell=data.frame()
for (k in 1:m) {
y1=longidata[1:73,k+2]
y2=apply(longidata[1:73,-c(1,2,k+2)],1,sum)
if (length(which(y1>0))<=5){next}
fm=try({glm(cbind(y1,y2)~bcell + bbymale + enrollment_age + imrbthwghtg_all +gestage_all+evercigpreg+alpha+deliver, data=longibcell[1:73,],family="binomial")},silent = T)
if (inherits(fm,"try-error")){
next()
}else{
fm=glm(cbind(y1,y2)~bcell + bbymale + enrollment_age + imrbthwghtg_all +gestage_all+evercigpreg+alpha+deliver ,data=longibcell[1:73,],family="binomial")
a=summary(fm)
r1=a$coefficients[2,1]
r2=a$coefficients[2,4]
r3= c(r1-1.96*a$coefficients[2,2],r1+ 1.96*a$coefficients[2,2])
rr=c(r1,r2,r3)
microbe=c(microbe,name[k])
rrbcell=rbind(rrbcell,rr)
}
}
colnames(rrbcell)=c("coef","pvalue","lower","upper")
fdr=p.adjust(rrbcell[,2],method = "BH")
rrbcell=data.frame(microbe,rrbcell,fdr)
rrbcell=rrbcell[order(rrbcell[,3]),]
rrbcellfdr=rrbcell[which(rrbcell[,6]<0.1),]
rrbcellfdr microbe coef pvalue lower
3 Akkermansia 0.149334920 0.000000e+00 0.143781505
6 Anaerostipes 0.118509617 0.000000e+00 0.116538258
9 Bacteroides 0.049470749 0.000000e+00 0.048840480
10 Bifidobacterium -0.024037349 0.000000e+00 -0.024814758
19 Clostridium_sensu_stricto -0.137420301 0.000000e+00 -0.139323763
20 Collinsella -0.256051819 0.000000e+00 -0.266603964
27 Enterobacter 0.117707378 0.000000e+00 0.115659423
29 Escherichia/Shigella 0.038638782 0.000000e+00 0.037533017
31 F__Enterobacteriaceae -0.107515227 0.000000e+00 -0.109814290
32 F__Erysipelotrichaceae -0.137490458 0.000000e+00 -0.143660183
33 F__Lachnospiraceae -0.117653074 0.000000e+00 -0.118862374
37 Fusicatenibacter -0.146038569 0.000000e+00 -0.152478569
39 Gemmiger -0.387513811 0.000000e+00 -0.394873753
45 Lactobacillus -0.114598354 0.000000e+00 -0.116944176
48 Parabacteroides -0.099252933 0.000000e+00 -0.102088187
49 Pseudomonas -0.727199084 0.000000e+00 -0.738190108
51 Romboutsia 0.611847621 0.000000e+00 0.593088281
54 Ruminococcus -0.211458858 0.000000e+00 -0.218515301
56 Staphylococcus 0.106439345 0.000000e+00 0.102575393
57 Streptococcus 0.140173803 0.000000e+00 0.138736848
59 Sutterella 0.248466080 0.000000e+00 0.236318570
25 Eggerthella -0.176481732 1.306545e-244 -0.186837699
60 Terrisporobacter 0.310955702 1.730412e-205 0.291030916
55 Ruminococcus2 0.072924910 4.044932e-196 0.068140695
28 Enterococcus 0.027844856 6.855783e-192 0.025997865
38 Gemella 0.255246726 3.772464e-146 0.235813634
13 Butyricicoccus -0.175167662 5.654264e-146 -0.188512110
30 Eubacterium -0.141573987 7.068964e-142 -0.152516062
50 Raoultella 0.347371187 2.432956e-117 0.317805369
53 Rothia 0.233370451 2.267660e-104 0.212287356
17 Clostridium_XVIII -0.020569192 6.646466e-95 -0.022519768
41 Haemophilus -0.069805539 1.166025e-73 -0.077341570
52 Roseburia 0.034312534 3.111392e-73 0.030597193
23 Dialister -0.390456229 1.460766e-68 -0.434190089
36 Flavonifractor -0.071390271 9.394189e-67 -0.079497113
44 Klebsiella -0.105455697 4.464931e-64 -0.117685737
8 Atopobium 0.237168552 1.058203e-51 0.206440794
16 Clostridium_XI 0.217282052 1.110131e-42 0.186181714
26 Eisenbergiella 0.093755706 3.393022e-39 0.079725692
63 Clostridium_XlVb -0.528191343 7.648430e-38 -0.608699066
18 Clostridium_XlVa 0.015012283 1.415467e-33 0.012575695
42 Hungatella 0.061185914 1.459965e-20 0.048285100
34 F__Ruminococcaceae -0.035741835 7.200112e-19 -0.043638128
11 Blautia 0.003819245 1.456835e-17 0.002941723
15 Clostridium_IV -0.034205005 5.379783e-16 -0.042479118
12 Buttiauxella -0.167637523 6.978166e-16 -0.208347918
5 Anaerococcus -0.158588239 3.407535e-13 -0.201301346
4 Alistipes 0.015534318 1.021333e-11 0.011059058
22 Corynebacterium 0.061094324 3.525047e-11 0.043013568
7 Anaerotruncus -0.149666398 1.182279e-10 -0.195205794
43 Intestinibacter -0.037128665 4.825503e-09 -0.049561808
58 Subdoligranulum 0.029369382 2.262715e-07 0.018248802
40 Granulicatella -0.045746523 1.517769e-04 -0.069415948
2 Actinomyces -0.012238722 2.006244e-03 -0.020003538
64 F__Peptostreptococcaceae 0.026416797 6.615948e-03 0.007350192
47 O__Clostridiales 0.067264510 6.921732e-03 0.018446064
46 Lactococcus 0.049462199 7.217583e-03 0.013377685
21 Coprobacillus -0.035736325 1.604381e-02 -0.064825030
35 Finegoldia -0.066841901 2.334336e-02 -0.124612421
65 Oscillibacter -0.031294105 4.900822e-02 -0.062452762
61 Varibaculum 0.075542942 5.455659e-02 -0.001477899
14 Chryseobacterium -0.115498221 5.999566e-02 -0.235858412
upper fdr
3 0.1548883347 0.000000e+00
6 0.1204809764 0.000000e+00
9 0.0501010180 0.000000e+00
10 -0.0232599390 0.000000e+00
19 -0.1355168394 0.000000e+00
20 -0.2454996741 0.000000e+00
27 0.1197553323 0.000000e+00
29 0.0397445464 0.000000e+00
31 -0.1052161640 0.000000e+00
32 -0.1313207320 0.000000e+00
33 -0.1164437737 0.000000e+00
37 -0.1395985692 0.000000e+00
39 -0.3801538687 0.000000e+00
45 -0.1122525322 0.000000e+00
48 -0.0964176795 0.000000e+00
49 -0.7162080606 0.000000e+00
51 0.6306069597 0.000000e+00
54 -0.2044024150 0.000000e+00
56 0.1103032970 0.000000e+00
57 0.1416107575 0.000000e+00
59 0.2606135909 0.000000e+00
25 -0.1661257654 3.860245e-244
60 0.3308804876 4.890295e-205
55 0.0777091253 1.095503e-195
28 0.0296918479 1.782503e-191
38 0.2746798183 9.431159e-146
13 -0.1618232141 1.361212e-145
30 -0.1306319120 1.641009e-141
50 0.3769370053 5.453176e-117
53 0.2544535456 4.913263e-104
17 -0.0186186153 1.393614e-94
41 -0.0622695084 2.368489e-73
52 0.0380278749 6.128499e-73
23 -0.3467223687 2.792640e-68
36 -0.0632834295 1.744635e-66
44 -0.0932256570 8.061682e-64
8 0.2678963101 1.859005e-51
16 0.2483823909 1.898909e-42
26 0.1077857202 5.655036e-39
63 -0.4476836191 1.242870e-37
18 0.0174488709 2.244033e-33
42 0.0740867285 2.259469e-20
34 -0.0278455407 1.088389e-18
11 0.0046967659 2.152142e-17
15 -0.0259308919 7.770798e-16
12 -0.1269271271 9.860453e-16
5 -0.1158751311 4.712548e-13
4 0.0200095767 1.383055e-11
22 0.0791750804 4.676083e-11
7 -0.1041270019 1.536963e-10
43 -0.0246955230 6.150151e-09
58 0.0404899621 2.828393e-07
40 -0.0220770989 1.861415e-04
2 -0.0044739063 2.414924e-03
64 0.0454834033 7.818848e-03
47 0.1160829558 8.034153e-03
46 0.0855467138 8.230577e-03
21 -0.0066476206 1.798013e-02
35 -0.0090713806 2.571726e-02
65 -0.0001354472 5.309224e-02
61 0.1525637833 5.813407e-02
14 0.0048619705 6.289868e-02options(warn = 2)
m=ncol(longidata)-2
n=nrow(longidata)
name=colnames(longidata)[-c(1,2)]
microbe=c()
rrbcell=data.frame()
for (k in 1:m) {
y1=longidata[1:73,k+2]
y2=apply(longidata[1:73,-c(1,2,k+2)],1,sum)
if (length(which(y1>0))<=5){next}
fm=try({glm(cbind(y1,y2)~cd4t + bbymale + enrollment_age + imrbthwghtg_all +gestage_all+evercigpreg+alpha+deliver, data=longicd4[1:73,],family="binomial")},silent = T)
if (inherits(fm,"try-error")){
next()
}else{
fm=glm(cbind(y1,y2)~cd4t + bbymale + enrollment_age + imrbthwghtg_all +gestage_all+evercigpreg+alpha+deliver , data=longicd4[1:73,],family="binomial")
a=summary(fm)
r1=a$coefficients[2,1]
r2=a$coefficients[2,4]
r3= c(r1-1.96*a$coefficients[2,2],r1+ 1.96*a$coefficients[2,2])
rr=c(r1,r2,r3)
microbe=c(microbe,name[k])
rrbcell=rbind(rrbcell,rr)
}
}
colnames(rrbcell)=c("coef","pvalue","lower","upper")
fdr=p.adjust(rrbcell[,2],method = "BY")
rrbcell=data.frame(microbe,rrbcell,fdr)
rrbcell=rrbcell[order(rrbcell[,3]),]
rrbcellfdr=rrbcell[which(rrbcell[,6]<0.1),]
rrbcellfdr microbe coef pvalue lower
2 Actinomyces 0.169468334 0.000000e+00 0.161434092
4 Alistipes 0.258233974 0.000000e+00 0.252701146
6 Anaerostipes 0.046550826 0.000000e+00 0.044420085
9 Bacteroides 0.016083607 0.000000e+00 0.015584220
10 Bifidobacterium -0.048958699 0.000000e+00 -0.049506147
11 Blautia -0.055319840 0.000000e+00 -0.056052611
15 Clostridium_IV -0.102045759 0.000000e+00 -0.106336164
16 Clostridium_XVIII -0.074619301 0.000000e+00 -0.075734927
18 Clostridium_sensu_stricto -0.306255987 0.000000e+00 -0.308219728
19 Collinsella -0.150544513 0.000000e+00 -0.155611406
25 Eisenbergiella -0.228045376 0.000000e+00 -0.239314243
26 Enterobacter -0.059201302 0.000000e+00 -0.061785183
27 Enterococcus 0.075023950 0.000000e+00 0.073967662
28 Escherichia/Shigella 0.052023599 0.000000e+00 0.051260996
30 F__Enterobacteriaceae -0.029688047 0.000000e+00 -0.031010897
32 F__Lachnospiraceae -0.205569200 0.000000e+00 -0.206651884
39 Haemophilus -0.202027505 0.000000e+00 -0.208645479
42 Klebsiella -0.272495890 0.000000e+00 -0.280678159
48 Robinsoniella -0.284077737 0.000000e+00 -0.292698413
49 Romboutsia -0.273134544 0.000000e+00 -0.283221723
53 Ruminococcus2 0.146804050 0.000000e+00 0.144620807
54 Staphylococcus 0.066345681 0.000000e+00 0.063469306
55 Streptococcus 0.053305462 0.000000e+00 0.052192474
56 Sutterella -0.488966545 0.000000e+00 -0.514054785
57 Terrisporobacter -0.393701988 0.000000e+00 -0.408095506
59 Veillonella -0.168230677 0.000000e+00 -0.170037230
1 Acinetobacter 0.226535139 2.148910e-276 0.214036043
46 Parabacteroides -0.035784893 2.819603e-272 -0.037774321
41 Intestinibacter -0.176916806 8.328824e-248 -0.187230564
33 F__Ruminococcaceae 0.086283452 2.893897e-227 0.081028911
50 Roseburia 0.043101165 4.637906e-146 0.039818656
17 Clostridium_XlVa -0.015165748 5.871137e-140 -0.016346016
35 Flavonifractor 0.033967910 4.011365e-107 0.030939608
3 Akkermansia -0.061558578 1.729687e-97 -0.067316693
24 Eggerthella -0.056400743 2.385908e-50 -0.063809176
29 Eubacterium 0.061543819 2.576607e-49 0.053372422
21 Corynebacterium 0.139282839 1.812262e-47 0.120419646
40 Hungatella 0.072921955 8.133089e-47 0.062974853
43 Lactobacillus 0.009729548 3.303401e-38 0.008253984
36 Fusicatenibacter -0.027422516 5.288156e-32 -0.031987340
61 F__Peptostreptococcaceae -0.086586947 4.032397e-26 -0.102640265
38 Granulicatella -0.122117462 4.883448e-20 -0.148228694
60 Clostridium_XlVb -0.206010980 2.855736e-16 -0.255377443
31 F__Erysipelotrichaceae 0.012747780 7.552224e-16 0.009648302
58 Varibaculum 0.169309422 2.971702e-15 0.127261432
5 Anaerococcus 0.100210796 6.336238e-14 0.074025652
20 Coprobacillus 0.057318263 2.105391e-10 0.039635933
34 Finegoldia -0.096707637 4.807014e-09 -0.129088245
13 Butyricicoccus 0.018541059 2.305580e-05 0.009956091
51 Rothia -0.035521905 5.283210e-05 -0.052743661
52 Ruminococcus -0.009002478 7.461567e-05 -0.013457050
7 Anaerotruncus -0.051184371 2.775431e-04 -0.078780013
22 Dialister -0.069491125 3.901966e-04 -0.107894545
44 Lactococcus 0.027805321 8.573952e-04 0.011456946
37 Gemella -0.024331427 7.637783e-03 -0.042208259
upper fdr
2 0.177502575 0.000000e+00
4 0.263766803 0.000000e+00
6 0.048681567 0.000000e+00
9 0.016582993 0.000000e+00
10 -0.048411251 0.000000e+00
11 -0.054587069 0.000000e+00
15 -0.097755354 0.000000e+00
16 -0.073503675 0.000000e+00
18 -0.304292246 0.000000e+00
19 -0.145477621 0.000000e+00
25 -0.216776508 0.000000e+00
26 -0.056617422 0.000000e+00
27 0.076080239 0.000000e+00
28 0.052786202 0.000000e+00
30 -0.028365196 0.000000e+00
32 -0.204486516 0.000000e+00
39 -0.195409531 0.000000e+00
42 -0.264313621 0.000000e+00
48 -0.275457062 0.000000e+00
49 -0.263047365 0.000000e+00
53 0.148987293 0.000000e+00
54 0.069222056 0.000000e+00
55 0.054418449 0.000000e+00
56 -0.463878305 0.000000e+00
57 -0.379308470 0.000000e+00
59 -0.166424123 0.000000e+00
1 0.239034234 2.325347e-275
46 -0.033795466 2.942138e-271
41 -0.166603048 8.391099e-247
33 0.091537992 2.818350e-226
50 0.046383674 4.371127e-145
17 -0.013985480 5.360501e-139
35 0.036996212 3.551497e-106
3 -0.055800463 1.486352e-96
24 -0.048992310 1.991677e-49
29 0.069715217 2.091120e-48
21 0.158146033 1.431042e-46
40 0.082869057 6.253240e-46
43 0.011205111 2.474742e-37
36 -0.022857693 3.862580e-31
61 -0.070533629 2.873509e-25
38 -0.096006231 3.397117e-19
60 -0.156644518 1.940362e-15
31 0.015847258 5.014820e-15
58 0.211357411 1.929416e-14
5 0.126395940 4.024453e-13
20 0.075000593 1.308784e-09
34 -0.064327029 2.925953e-08
13 0.027126027 1.374730e-04
51 -0.018300150 3.087174e-04
52 -0.004547906 4.274576e-04
7 -0.023588728 1.559410e-03
22 -0.031087705 2.151002e-03
44 0.044153695 4.638958e-03
37 -0.006454596 4.057307e-02options(warn = 2)
m=ncol(longidata)-2
n=nrow(longidata)
name=colnames(longidata)[-c(1,2)]
microbe=c()
rrbcell=data.frame()
for (k in 1:m) {
y1=longidata[1:73,k+2]
y2=apply(longidata[1:73,-c(1,2,k+2)],1,sum)
if (length(which(y1>0))<=5){next}
fm=try({glm(cbind(y1,y2)~cd8t + bbymale + enrollment_age + imrbthwghtg_all +gestage_all+evercigpreg+alpha+deliver , data=longicd8[1:73,],family="binomial")},silent = T)
if (inherits(fm,"try-error")){
next()
}else{
fm=glm(cbind(y1,y2)~cd8t + bbymale + enrollment_age + imrbthwghtg_all +gestage_all+evercigpreg+alpha+deliver , data=longicd8[1:73,],family="binomial")
a=summary(fm)
r1=a$coefficients[2,1]
r2=a$coefficients[2,4]
r3= c(r1-1.96*a$coefficients[2,2],r1+ 1.96*a$coefficients[2,2])
rr=c(r1,r2,r3)
microbe=c(microbe,name[k])
rrbcell=rbind(rrbcell,rr)
}
}
colnames(rrbcell)=c("coef","pvalue","lower","upper")
fdr=p.adjust(rrbcell[,2],method = "BY")
rrbcell=data.frame(microbe,rrbcell,fdr)
rrbcell=rrbcell[order(rrbcell[,3]),]
rrbcellfdr=rrbcell[which(rrbcell[,6]<0.1),]
rrbcellfdr microbe coef pvalue lower
1 Acinetobacter 1.021832063 0.000000e+00 0.99677296
4 Alistipes 0.169406604 0.000000e+00 0.16446516
6 Anaerostipes 0.070012580 0.000000e+00 0.06737950
9 Bifidobacterium 0.068626512 0.000000e+00 0.06770159
10 Blautia -0.129621252 0.000000e+00 -0.13090626
22 Eggerthella -0.236311877 0.000000e+00 -0.24847464
24 Enterobacter 0.300700773 0.000000e+00 0.29759874
25 Enterococcus 0.069361319 0.000000e+00 0.06729827
26 Escherichia/Shigella 0.034157356 0.000000e+00 0.03294529
28 F__Enterobacteriaceae -0.077983865 0.000000e+00 -0.08027303
40 Intestinibacter 0.215227922 0.000000e+00 0.20446910
41 Klebsiella -0.357857886 0.000000e+00 -0.37080232
44 Parabacteroides -0.100579544 0.000000e+00 -0.10402502
46 Prevotella -0.309452102 0.000000e+00 -0.32224470
50 Romboutsia 0.543125212 0.000000e+00 0.52909022
51 Roseburia 0.125171485 0.000000e+00 0.12132390
55 Staphylococcus 0.081671414 0.000000e+00 0.07779739
56 Streptococcus 0.194237458 0.000000e+00 0.19259549
59 Terrisporobacter 0.267168805 0.000000e+00 0.25419334
53 Ruminococcus -0.114314048 7.929215e-295 -0.12041948
3 Akkermansia -0.163948816 2.931380e-262 -0.17323724
33 Flavonifractor -0.135020218 2.891424e-222 -0.14333560
47 Pseudomonas -0.107104732 1.749476e-204 -0.11398458
61 Veillonella 0.038284691 2.021478e-186 0.03570781
35 Gemella 0.362030365 3.692348e-169 0.33643499
12 Butyricicoccus -0.164530165 1.459985e-164 -0.17632574
57 Subdoligranulum -0.188531200 3.053235e-146 -0.20288036
52 Rothia 0.321624310 3.322110e-142 0.29679546
30 F__Lachnospiraceae -0.016973828 2.211343e-126 -0.01836503
8 Bacteroides 0.008738623 1.809129e-93 0.00790347
20 Dialister -0.832357175 8.622516e-88 -0.91449359
63 F__Peptostreptococcaceae 0.182090933 2.957221e-75 0.16264777
58 Sutterella 0.169439420 1.949717e-71 0.15085718
17 Clostridium_sensu_stricto 0.017757138 2.318987e-66 0.01573457
15 Clostridium_XVIII -0.016545962 1.339653e-55 -0.01861056
27 Eubacterium -0.095590687 5.019352e-53 -0.10781443
16 Clostridium_XlVa -0.020061744 3.404540e-48 -0.02275739
54 Ruminococcus2 0.032982766 1.430779e-47 0.02852089
18 Coprobacillus -0.236971608 3.533682e-47 -0.26916720
5 Anaerococcus -0.291147663 3.461158e-37 -0.33593313
23 Eisenbergiella 0.085978573 3.725394e-36 0.07255634
7 Anaerotruncus -0.363389342 7.576677e-35 -0.42122752
34 Fusicatenibacter 0.030502899 2.152433e-27 0.02498915
43 O__Clostridiales -0.491245548 2.704845e-25 -0.58390037
37 Granulicatella 0.120174620 2.207071e-17 0.09240608
29 F__Erysipelotrichaceae -0.024242864 7.120860e-17 -0.02993681
31 F__Ruminococcaceae -0.028784589 2.384399e-16 -0.03566399
36 Gemmiger -0.019858442 3.215198e-14 -0.02498702
32 Finegoldia -0.198507198 6.339704e-12 -0.25512615
19 Corynebacterium 0.081060185 9.913668e-11 0.05649749
42 Lactococcus 0.115584213 8.171535e-10 0.07869699
62 Clostridium_XlVb -0.215127612 1.856672e-09 -0.28528717
14 Clostridium_IV -0.022444379 1.599048e-08 -0.03022959
2 Actinomyces 0.025171755 3.154916e-04 0.01147564
60 Varibaculum -0.139754293 8.657906e-04 -0.22199091
39 Hungatella -0.016493013 1.027218e-02 -0.02908835
upper fdr
1 1.046891164 0.000000e+00
4 0.174348050 0.000000e+00
6 0.072645661 0.000000e+00
9 0.069551430 0.000000e+00
10 -0.128336248 0.000000e+00
22 -0.224149112 0.000000e+00
24 0.303802809 0.000000e+00
25 0.071424367 0.000000e+00
26 0.035369419 0.000000e+00
28 -0.075694698 0.000000e+00
40 0.225986746 0.000000e+00
41 -0.344913447 0.000000e+00
44 -0.097134070 0.000000e+00
46 -0.296659501 0.000000e+00
50 0.557160206 0.000000e+00
51 0.129019071 0.000000e+00
55 0.085545440 0.000000e+00
56 0.195879422 0.000000e+00
59 0.280144274 0.000000e+00
53 -0.108208620 1.203691e-293
3 -0.154660389 4.238064e-261
33 -0.126704835 3.990284e-221
47 -0.100224879 2.309377e-203
61 0.040861572 2.557246e-185
35 0.387625739 4.484121e-168
12 -0.152734588 1.704864e-163
57 -0.174182036 3.433295e-145
52 0.346453156 3.602224e-141
30 -0.015582624 2.315116e-125
8 0.009573775 1.830893e-92
20 -0.750220766 8.444753e-87
63 0.201534095 2.805747e-74
58 0.188021658 1.793793e-70
17 0.019779704 2.070780e-65
15 -0.014481363 1.162088e-54
27 -0.083366946 4.233112e-52
16 -0.017366099 2.793646e-47
54 0.037444641 1.143151e-46
18 -0.204776018 2.750917e-46
5 -0.246362198 2.627097e-36
23 0.099400809 2.758690e-35
7 -0.305551160 5.477018e-34
34 0.036016646 1.519763e-26
43 -0.398590723 1.866399e-24
37 0.147943163 1.489081e-16
29 -0.018548920 4.699907e-16
31 -0.021905190 1.540266e-15
36 -0.014729866 2.033673e-13
32 -0.141888242 3.928146e-11
19 0.105622884 6.019758e-10
42 0.152471435 4.864611e-09
62 -0.144968055 1.084043e-08
14 -0.014659168 9.160103e-08
2 0.038867869 1.773817e-03
60 -0.057517676 4.779306e-03
39 -0.003897677 5.569153e-02options(warn = 2)
m=ncol(longidata)-2
n=nrow(longidata)
name=colnames(longidata)[-c(1,2)]
microbe=c()
rrbcell=data.frame()
for (k in 1:m) {
y1=longidata[1:73,k+2]
y2=apply(longidata[1:73,-c(1,2,k+2)],1,sum)
if (length(which(y1>0))<=5) {next}
fm=try({glm(cbind(y1,y2)~mono + bbymale + enrollment_age + imrbthwghtg_all +gestage_all+evercigpreg+alpha+deliver , data=longimono[1:73,],family="binomial")},silent = T)
if (inherits(fm,"try-error")){
next()
}else{
fm=glm(cbind(y1,y2)~mono + bbymale + enrollment_age + imrbthwghtg_all +gestage_all+evercigpreg+alpha+deliver , data=longimono[1:73,],family="binomial")
a=summary(fm)
r1=a$coefficients[2,1]
r2=a$coefficients[2,4]
r3= c(r1-1.96*a$coefficients[2,2],r1+ 1.96*a$coefficients[2,2])
rr=c(r1,r2,r3)
microbe=c(microbe,name[k])
rrbcell=rbind(rrbcell,rr)
}
}
colnames(rrbcell)=c("coef","pvalue","lower","upper")
fdr=p.adjust(rrbcell[,2],method = "BH")
rrbcell=data.frame(microbe,rrbcell,fdr)
rrbcell=rrbcell[order(rrbcell[,3]),]
rrbcellfdr=rrbcell[which(rrbcell[,6]<0.1),]
rrbcellfdr microbe coef pvalue lower upper
3 Alistipes -1.29796297 0.000000e+00 -1.32826167 -1.267664263
9 Bifidobacterium -0.08109602 0.000000e+00 -0.08243385 -0.079758186
10 Blautia -0.05772084 0.000000e+00 -0.05939462 -0.056047060
14 Clostridium_IV 0.18796079 0.000000e+00 0.17972916 0.196192420
15 Clostridium_XVIII 0.05954386 0.000000e+00 0.05688059 0.062207128
16 Clostridium_XlVa 0.13405667 0.000000e+00 0.13077178 0.137341559
17 Clostridium_sensu_stricto 0.37422664 0.000000e+00 0.37114636 0.377306921
24 Eisenbergiella 0.50062430 0.000000e+00 0.47796861 0.523279987
25 Enterobacter -0.15988059 0.000000e+00 -0.16503079 -0.154730384
26 Enterococcus 0.07429574 0.000000e+00 0.07117348 0.077417991
27 Escherichia/Shigella 0.19405655 0.000000e+00 0.19238384 0.195729259
29 F__Enterobacteriaceae -0.41621935 0.000000e+00 -0.41932971 -0.413108987
31 F__Lachnospiraceae -0.28065733 0.000000e+00 -0.28301955 -0.278295109
32 F__Ruminococcaceae -0.38377207 0.000000e+00 -0.40303059 -0.364513545
33 Faecalibacterium -0.44089510 0.000000e+00 -0.44500125 -0.436788953
35 Flavonifractor 0.17666309 0.000000e+00 0.16866822 0.184657965
38 Gemmiger 0.23759227 0.000000e+00 0.22814466 0.247039871
41 Hungatella 0.80621912 0.000000e+00 0.77560880 0.836829440
42 Intestinibacter -0.38153507 0.000000e+00 -0.40074627 -0.362323879
44 Lactobacillus -0.37088449 0.000000e+00 -0.37511365 -0.366655325
47 Prevotella -0.47008133 0.000000e+00 -0.49214916 -0.448013505
48 Pseudomonas -1.48293969 0.000000e+00 -1.50724433 -1.458635044
49 Raoultella 0.85318625 0.000000e+00 0.82765911 0.878713394
51 Roseburia 0.18946815 0.000000e+00 0.18251477 0.196421527
55 Staphylococcus 0.23888751 0.000000e+00 0.23304523 0.244729796
56 Streptococcus -0.08042891 0.000000e+00 -0.08283760 -0.078020230
61 Veillonella 0.21146126 0.000000e+00 0.20769621 0.215226314
40 Haemophilus 0.29081009 9.051301e-293 0.27522325 0.306396924
5 Anaerostipes -0.08749543 4.332766e-277 -0.09231688 -0.082673969
2 Actinomyces -0.46683220 2.967269e-252 -0.49380413 -0.439860265
36 Fusicatenibacter -0.14396638 2.679923e-195 -0.15343130 -0.134501459
8 Bacteroides -0.01682654 5.085331e-180 -0.01797929 -0.015673781
18 Collinsella -0.19442816 2.721098e-178 -0.20781324 -0.181043082
1 Acinetobacter 0.26552580 2.894569e-173 0.24697971 0.284071896
58 Sutterella 0.36019767 1.020450e-148 0.33301526 0.387380081
21 Dialister 0.63409238 2.023615e-126 0.58212912 0.686055636
28 Eubacterium -0.18275698 2.767283e-94 -0.20014585 -0.165368113
30 F__Erysipelotrichaceae 0.07877469 3.734290e-88 0.07101765 0.086531719
63 F__Peptostreptococcaceae -0.34444871 1.602269e-79 -0.38020326 -0.308694156
57 Subdoligranulum -0.17503171 7.354200e-68 -0.19474047 -0.155322957
54 Ruminococcus2 0.05189924 1.106850e-51 0.04517382 0.058624670
19 Coprobacillus -0.45125629 1.397839e-51 -0.50979237 -0.392720210
7 Atopobium 0.34574440 2.181366e-51 0.30080782 0.390680985
20 Corynebacterium 0.27583956 4.666034e-49 0.23911558 0.312563538
37 Gemella -0.29327161 1.014146e-44 -0.33424034 -0.252302876
53 Ruminococcus 0.08294016 3.139490e-43 0.07114740 0.094732923
62 Clostridium_XlVb 0.43549745 4.181567e-41 0.37192753 0.499067366
52 Rothia -0.25502274 2.729297e-36 -0.29475683 -0.215288641
64 Oscillibacter -0.39582559 8.764872e-35 -0.45888665 -0.332764540
4 Anaerococcus -0.22829340 5.527150e-17 -0.28172152 -0.174865282
46 O__Clostridiales -0.41698107 5.439899e-13 -0.53027493 -0.303687199
11 Buttiauxella 0.14481503 4.681006e-09 0.09636316 0.193266892
50 Romboutsia -0.04302995 5.188245e-09 -0.05746899 -0.028590911
39 Granulicatella -0.12697034 7.515988e-09 -0.17003370 -0.083906967
6 Anaerotruncus -0.12312214 8.843026e-05 -0.18467814 -0.061566148
13 Chryseobacterium 0.36761410 8.924773e-05 0.18371816 0.551510028
45 Lactococcus -0.07987191 3.905138e-04 -0.12401480 -0.035729011
43 Klebsiella -0.01952662 3.959912e-04 -0.03032960 -0.008723636
34 Finegoldia -0.10867232 1.429202e-03 -0.17547026 -0.041874386
22 Dolosigranulum -0.19077390 1.460677e-02 -0.34389396 -0.037653836
60 Varibaculum -0.11527318 5.899468e-02 -0.23492760 0.004381246
fdr
3 0.000000e+00
9 0.000000e+00
10 0.000000e+00
14 0.000000e+00
15 0.000000e+00
16 0.000000e+00
17 0.000000e+00
24 0.000000e+00
25 0.000000e+00
26 0.000000e+00
27 0.000000e+00
29 0.000000e+00
31 0.000000e+00
32 0.000000e+00
33 0.000000e+00
35 0.000000e+00
38 0.000000e+00
41 0.000000e+00
42 0.000000e+00
44 0.000000e+00
47 0.000000e+00
48 0.000000e+00
49 0.000000e+00
51 0.000000e+00
55 0.000000e+00
56 0.000000e+00
61 0.000000e+00
40 2.068869e-292
5 9.561967e-277
2 6.330174e-252
36 5.532744e-195
8 1.017066e-179
18 5.277282e-178
1 5.448601e-173
58 1.865965e-148
21 3.597538e-126
28 4.786651e-94
30 6.289331e-88
63 2.629365e-79
57 1.176672e-67
54 1.727765e-51
19 2.130041e-51
7 3.246684e-51
20 6.786958e-49
37 1.442341e-44
53 4.367985e-43
62 5.694049e-41
52 3.639062e-36
64 1.144800e-34
4 7.074752e-17
46 6.826540e-13
11 5.761238e-09
50 6.265050e-09
39 8.907838e-09
6 1.019974e-04
13 1.019974e-04
45 4.369558e-04
43 4.369558e-04
34 1.550321e-03
22 1.558055e-02
60 6.189606e-02options(warn = 2)
m=ncol(longidata)-2
n=nrow(longidata)
name=colnames(longidata)[-c(1,2)]
microbe=c()
rrbcell=data.frame()
for (k in 1:m) {
y1=longidata[1:73,k+2]
y2=apply(longidata[1:73,-c(1,2,k+2)],1,sum)
if (length(which(y1>0))<=5) {next}
fm=try({glm(cbind(y1,y2)~nk + bbymale + enrollment_age + imrbthwghtg_all +gestage_all+evercigpreg+alpha+deliver , data=longink[1:73,],family="binomial")},silent = T)
if (inherits(fm,"try-error")){
next()
}else{
fm=glm(cbind(y1,y2)~nk + bbymale + enrollment_age + imrbthwghtg_all +gestage_all+evercigpreg+alpha+deliver, data=longink[1:73,],family="binomial")
a=summary(fm)
r1=a$coefficients[2,1]
r2=a$coefficients[2,4]
r3= c(r1-1.96*a$coefficients[2,2],r1+ 1.96*a$coefficients[2,2])
rr=c(r1,r2,r3)
microbe=c(microbe,name[k])
rrbcell=rbind(rrbcell,rr)
}
}
colnames(rrbcell)=c("coef","pvalue","lower","upper")
fdr=p.adjust(rrbcell[,2],method = "BH")
rrbcell=data.frame(microbe,rrbcell,fdr)
rrbcell=rrbcell[order(rrbcell[,3]),]
rrbcellfdr=rrbcell[which(rrbcell[,6]<0.1),]
rrbcellfdr microbe coef pvalue lower
8 Bacteroides -0.01955453 0.000000e+00 -0.020285491
9 Bifidobacterium -0.14419145 0.000000e+00 -0.145166842
10 Blautia 0.10797694 0.000000e+00 0.107068276
14 Clostridium_IV 0.20254868 0.000000e+00 0.197261701
15 Clostridium_XVIII 0.08314154 0.000000e+00 0.081627351
16 Clostridium_XlVa -0.04414908 0.000000e+00 -0.046414452
18 Collinsella -0.20306216 0.000000e+00 -0.213425531
24 Eisenbergiella 0.39116746 0.000000e+00 0.379762195
26 Enterococcus 0.06030545 0.000000e+00 0.058537750
27 Escherichia/Shigella -0.12418146 0.000000e+00 -0.125428124
29 F__Enterobacteriaceae 0.07357929 0.000000e+00 0.071931149
30 F__Erysipelotrichaceae 0.10910041 0.000000e+00 0.104696150
31 F__Lachnospiraceae 0.12862252 0.000000e+00 0.127374434
34 Flavonifractor -0.50677460 0.000000e+00 -0.515243010
35 Fusicatenibacter -0.20154831 0.000000e+00 -0.208629884
37 Gemmiger -0.69115755 0.000000e+00 -0.704706912
39 Haemophilus -0.27279802 0.000000e+00 -0.284181517
40 Hungatella -0.44498038 0.000000e+00 -0.466679192
43 Lactobacillus 0.09466972 0.000000e+00 0.092798059
47 Prevotella -0.89541949 0.000000e+00 -0.914293205
48 Robinsoniella -0.14725128 0.000000e+00 -0.154697191
54 Staphylococcus -0.14378067 0.000000e+00 -0.148516270
55 Streptococcus 0.03526891 0.000000e+00 0.033858458
56 Subdoligranulum 0.29461946 0.000000e+00 0.283746342
60 Veillonella 0.07466214 0.000000e+00 0.072384050
46 Parabacteroides 0.05878280 1.720479e-289 0.055614233
42 Klebsiella 0.11714173 2.071426e-280 0.110725238
1 Acinetobacter -0.27514958 1.176010e-245 -0.291260680
12 Butyricicoccus 0.21704071 2.474266e-203 0.203059339
20 Corynebacterium -0.59660125 1.033617e-175 -0.637977198
52 Ruminococcus 0.10412371 1.176963e-156 0.096470341
2 Actinomyces -0.18675606 6.749023e-143 -0.201137845
57 Sutterella -0.23100445 6.503353e-120 -0.250450290
53 Ruminococcus2 -0.04978998 4.900693e-82 -0.054876574
5 Anaerostipes 0.02686485 9.264365e-77 0.024025251
49 Romboutsia 0.08628000 7.403691e-63 0.076174323
4 Anaerococcus 0.25811915 4.263488e-62 0.227696438
44 Lactococcus -0.27024854 6.844585e-60 -0.302700176
21 Dialister -0.26820969 1.102562e-58 -0.300756546
50 Roseburia -0.03589805 2.082427e-51 -0.040562790
23 Eggerthella 0.05605849 9.573700e-48 0.048489363
17 Clostridium_sensu_stricto -0.01040233 1.061574e-42 -0.011890898
19 Coprobacillus -0.24475522 1.323630e-40 -0.280711606
28 Eubacterium 0.05355188 4.041659e-34 0.044933340
59 Varibaculum 0.34300519 3.589282e-27 0.280733920
11 Buttiauxella -0.13632477 9.816051e-23 -0.163551268
32 F__Ruminococcaceae -0.04763165 3.540220e-20 -0.057777952
36 Gemella 0.09769714 1.249028e-16 0.074566131
25 Enterobacter -0.01036563 3.957023e-16 -0.012861576
41 Intestinibacter -0.04621811 1.832677e-15 -0.057609651
33 Finegoldia 0.12579159 2.599343e-09 0.084389753
58 Terrisporobacter 0.03207848 2.363187e-07 0.019913039
63 Oscillibacter 0.06412276 5.117639e-06 0.036560656
6 Anaerotruncus 0.08195393 5.499643e-05 0.042128162
3 Alistipes 0.01149133 9.643035e-04 0.004667708
61 Clostridium_XlVb 0.09186038 1.664746e-03 0.034599518
22 Dolosigranulum 0.11632392 2.619774e-03 0.040556785
upper fdr
8 -0.018823576 0.000000e+00
9 -0.143216049 0.000000e+00
10 0.108885597 0.000000e+00
14 0.207835662 0.000000e+00
15 0.084655721 0.000000e+00
16 -0.041883708 0.000000e+00
18 -0.192698797 0.000000e+00
24 0.402572729 0.000000e+00
26 0.062073146 0.000000e+00
27 -0.122934800 0.000000e+00
29 0.075227436 0.000000e+00
30 0.113504680 0.000000e+00
31 0.129870606 0.000000e+00
34 -0.498306187 0.000000e+00
35 -0.194466735 0.000000e+00
37 -0.677608190 0.000000e+00
39 -0.261414518 0.000000e+00
40 -0.423281558 0.000000e+00
43 0.096541373 0.000000e+00
47 -0.876545785 0.000000e+00
48 -0.139805362 0.000000e+00
54 -0.139045079 0.000000e+00
55 0.036679355 0.000000e+00
56 0.305492570 0.000000e+00
60 0.076940222 0.000000e+00
46 0.061951366 4.168853e-289
42 0.123558224 4.833327e-280
1 -0.259038474 2.646022e-245
12 0.231022073 5.375129e-203
20 -0.555225302 2.170596e-175
52 0.111777082 2.391892e-156
2 -0.172374270 1.328714e-142
57 -0.211558612 1.241549e-119
53 -0.044703389 9.080695e-82
5 0.029704450 1.667586e-76
49 0.096385672 1.295646e-62
4 0.288541857 7.259453e-62
44 -0.237796895 1.134760e-59
21 -0.235662838 1.781062e-58
50 -0.031233309 3.279822e-51
23 0.063627625 1.471081e-47
17 -0.008913761 1.592360e-42
19 -0.208798826 1.939272e-40
28 0.062170410 5.786921e-34
59 0.405276462 5.024995e-27
11 -0.109098263 1.344372e-22
32 -0.037485343 4.745401e-20
36 0.120828150 1.639349e-16
25 -0.007869692 5.087601e-16
41 -0.034826571 2.309173e-15
33 0.167193425 3.210954e-09
58 0.044243919 2.863092e-07
63 0.091684858 6.083231e-06
6 0.121779695 6.416250e-05
3 0.018314962 1.104566e-03
61 0.149121252 1.872840e-03
22 0.192091059 2.895539e-03options(warn = 2)
m=ncol(longidata)-2
n=nrow(longidata)
name=colnames(longidata)[-c(1,2)]
microbe=c()
rrbcell=data.frame()
for (k in 1:m) {
y1=longidata[1:73,k+2]
y2=apply(longidata[1:73,-c(1,2,k+2)],1,sum)
if (length(which(y1>0))<=5) {next}
fm=try({glm(cbind(y1,y2)~nrbc + bbymale + enrollment_age + imrbthwghtg_all +gestage_all+evercigpreg+alpha+deliver , data=longinrbc[1:73,],family="binomial")},silent = T)
if (inherits(fm,"try-error")){
next()
}else{
fm=glm(cbind(y1,y2)~nrbc + bbymale + enrollment_age + imrbthwghtg_all +gestage_all+evercigpreg+alpha+deliver , data=longinrbc[1:73,],family="binomial")
a=summary(fm)
r1=a$coefficients[2,1]
r2=a$coefficients[2,4]
r3= c(r1-1.96*a$coefficients[2,2],r1+ 1.96*a$coefficients[2,2])
rr=c(r1,r2,r3)
microbe=c(microbe,name[k])
rrbcell=rbind(rrbcell,rr)
}
}
colnames(rrbcell)=c("coef","pvalue","lower","upper")
fdr=round(p.adjust(rrbcell[,2],method = "BH"),3)
rrbcell=data.frame(microbe,rrbcell,fdr)
rrbcell=rrbcell[order(rrbcell[,3]),]
rrbcellfdr=rrbcell[which(rrbcell[,6]<0.1),]
rrbcellfdr microbe coef pvalue lower
1 Actinomyces -0.103140204 0.000000e+00 -0.1082694765
3 Anaerostipes 0.076041824 0.000000e+00 0.0746420423
5 Bacteroides -0.022549501 0.000000e+00 -0.0228940860
6 Bifidobacterium 0.017454224 0.000000e+00 0.0171197756
7 Blautia 0.073613573 0.000000e+00 0.0731682934
10 Clostridium_IV 0.064246158 0.000000e+00 0.0614103143
11 Clostridium_XVIII 0.017556831 0.000000e+00 0.0170482518
13 Clostridium_sensu_stricto -0.104865307 0.000000e+00 -0.1058154622
14 Collinsella 0.081213666 0.000000e+00 0.0789110232
20 Eisenbergiella 0.234643967 0.000000e+00 0.2275918881
22 Enterococcus -0.062341977 0.000000e+00 -0.0629729632
23 Escherichia/Shigella -0.061074067 0.000000e+00 -0.0616802460
25 F__Enterobacteriaceae 0.048597645 0.000000e+00 0.0478816956
27 F__Lachnospiraceae 0.084778434 0.000000e+00 0.0841635691
31 Fusicatenibacter -0.218006454 0.000000e+00 -0.2233728361
39 Lactobacillus 0.030188176 0.000000e+00 0.0294201766
43 Prevotella -0.153790852 0.000000e+00 -0.1600575290
45 Roseburia -0.059787544 0.000000e+00 -0.0615310565
48 Ruminococcus2 -0.049393210 0.000000e+00 -0.0505938405
49 Staphylococcus -0.079601768 0.000000e+00 -0.0819700409
50 Streptococcus 0.035710085 0.000000e+00 0.0350871508
38 Klebsiella 0.044792021 6.141336e-254 0.0422127637
30 Flavonifractor 0.032913232 8.093694e-254 0.0310175395
42 Parabacteroides 0.029481574 1.033481e-245 0.0277555097
15 Coprobacillus 0.203391973 1.013246e-196 0.1900691322
33 Gemmiger -0.049415486 1.686055e-169 -0.0529055842
17 Dialister -0.136311111 1.593396e-141 -0.1468597443
36 Hungatella -0.089697474 3.445573e-114 -0.0974383431
16 Corynebacterium -0.218118613 3.358352e-102 -0.2380359949
28 F__Ruminococcaceae 0.054430669 3.204368e-90 0.0491339000
52 Terrisporobacter -0.087755871 9.026485e-88 -0.0964165597
51 Sutterella 0.054957665 1.370776e-82 0.0493624179
35 Haemophilus -0.040146258 3.318968e-71 -0.0445563825
26 F__Erysipelotrichaceae -0.017387919 7.190716e-71 -0.0193026488
19 Eggerthella 0.033332133 3.140379e-65 0.0295018102
47 Ruminococcus -0.027308926 5.739011e-34 -0.0317143293
29 Finegoldia 0.094398867 3.576726e-20 0.0742879856
8 Buttiauxella -0.079247537 9.379993e-18 -0.0973479440
32 Gemella 0.034943538 2.224476e-12 0.0251867164
37 Intestinibacter -0.011022180 1.227596e-11 -0.0142099788
53 Veillonella 0.003390962 9.297214e-11 0.0023649775
56 Oscillibacter 0.037698282 3.839906e-07 0.0231439003
12 Clostridium_XlVa -0.001521128 3.443734e-06 -0.0021633399
41 O__Clostridiales -0.040725115 3.079922e-05 -0.0598784938
9 Butyricicoccus 0.013033891 1.456638e-04 0.0063082233
40 Lactococcus -0.016959140 9.177899e-04 -0.0269875163
34 Granulicatella -0.027715875 1.076074e-03 -0.0443292481
55 F__Peptostreptococcaceae -0.010468703 1.418685e-03 -0.0168992263
2 Alistipes -0.005421682 1.451214e-03 -0.0087588701
21 Enterobacter 0.001632824 4.067330e-03 0.0005188471
24 Eubacterium 0.005634843 3.081601e-02 0.0005204198
54 Clostridium_XlVb 0.021242899 8.203046e-02 -0.0026993070
upper fdr
1 -0.0980109320 0.000
3 0.0774416066 0.000
5 -0.0222049152 0.000
6 0.0177886715 0.000
7 0.0740588536 0.000
10 0.0670820013 0.000
11 0.0180654106 0.000
13 -0.1039151520 0.000
14 0.0835163091 0.000
20 0.2416960467 0.000
22 -0.0617109913 0.000
23 -0.0604678889 0.000
25 0.0493135943 0.000
27 0.0853932995 0.000
31 -0.2126400722 0.000
39 0.0309561751 0.000
43 -0.1475241751 0.000
45 -0.0580440323 0.000
48 -0.0481925800 0.000
49 -0.0772334946 0.000
50 0.0363330200 0.000
38 0.0473712784 0.000
30 0.0348089251 0.000
42 0.0312076391 0.000
15 0.2167148146 0.000
33 -0.0459253883 0.000
17 -0.1257624786 0.000
36 -0.0819566054 0.000
16 -0.1982012306 0.000
28 0.0597274376 0.000
52 -0.0790951815 0.000
51 0.0605529126 0.000
35 -0.0357361328 0.000
26 -0.0154731898 0.000
19 0.0371624566 0.000
47 -0.0229035229 0.000
29 0.1145097475 0.000
8 -0.0611471308 0.000
32 0.0447003604 0.000
37 -0.0078343822 0.000
53 0.0044169469 0.000
56 0.0522526637 0.000
12 -0.0008789156 0.000
41 -0.0215717371 0.000
9 0.0197595595 0.000
40 -0.0069307636 0.001
34 -0.0111025016 0.001
55 -0.0040381793 0.002
2 -0.0020844937 0.002
21 0.0027468002 0.005
24 0.0107492652 0.034
54 0.0451851043 0.088options(warn = 2)
m=ncol(longidata)-2
n=nrow(longidata)
name=colnames(longidata)[-c(1,2)]
microbe=c()
rrbcell=data.frame()
for (k in 1:m) {
y1=longidata[1:73,k+2]
y2=apply(longidata[1:73,-c(1,2,k+2)],1,sum)
if (length(which(y1>0))<=5) {next}
fm=try({glm(cbind(y1,y2)~gran + bbymale + enrollment_age + imrbthwghtg_all +gestage_all+evercigpreg+alpha+deliver , data=longigran[1:73,],family="binomial")},silent = T)
if (inherits(fm,"try-error")){
next()
}else{
fm=glm(cbind(y1,y2)~gran + bbymale + enrollment_age + imrbthwghtg_all +gestage_all+evercigpreg+alpha+deliver , data=longigran[1:73,],family="binomial")
a=summary(fm)
r1=a$coefficients[2,1]
r2=a$coefficients[2,4]
r3= c(r1-1.96*a$coefficients[2,2],r1+ 1.96*a$coefficients[2,2])
rr=round(c(r1,r2,r3),3)
microbe=c(microbe,name[k])
rrbcell=rbind(rrbcell,rr)
}
}
colnames(rrbcell)=c("coef","pvalue","lower","upper")
fdr=round(p.adjust(rrbcell[,2],method = "BH"),3)
rrbcell=data.frame(microbe,rrbcell,fdr)
rrbcell=rrbcell[order(rrbcell[,3]),]
rrbcellfdr=rrbcell[which(rrbcell[,6]<0.1),]
rrbcellfdr microbe coef pvalue lower upper fdr
1 Acinetobacter 0.017 0.000 0.013 0.022 0.000
2 Actinomyces 0.018 0.000 0.015 0.021 0.000
3 Akkermansia -0.032 0.000 -0.033 -0.030 0.000
4 Alistipes -0.057 0.000 -0.059 -0.055 0.000
5 Anaerococcus 0.053 0.000 0.038 0.068 0.000
6 Anaerostipes -0.052 0.000 -0.053 -0.051 0.000
8 Atopobium -0.041 0.000 -0.049 -0.034 0.000
9 Bacteroides 0.003 0.000 0.003 0.003 0.000
10 Bifidobacterium 0.020 0.000 0.020 0.020 0.000
11 Blautia -0.035 0.000 -0.035 -0.035 0.000
12 Buttiauxella 0.065 0.000 0.052 0.078 0.000
13 Butyricicoccus 0.011 0.000 0.006 0.016 0.000
14 Chryseobacterium -0.066 0.000 -0.092 -0.039 0.000
15 Clostridium_IV -0.055 0.000 -0.057 -0.053 0.000
16 Clostridium_XVIII 0.002 0.000 0.001 0.002 0.000
17 Clostridium_XlVa 0.012 0.000 0.012 0.013 0.000
18 Clostridium_sensu_stricto 0.059 0.000 0.059 0.060 0.000
19 Collinsella 0.016 0.000 0.013 0.018 0.000
20 Coprobacillus -0.042 0.000 -0.050 -0.034 0.000
21 Corynebacterium 0.061 0.000 0.051 0.070 0.000
22 Dialister 0.093 0.000 0.085 0.100 0.000
24 Eggerthella 0.011 0.000 0.009 0.014 0.000
25 Eisenbergiella -0.113 0.000 -0.116 -0.109 0.000
26 Enterobacter -0.017 0.000 -0.017 -0.016 0.000
27 Enterococcus 0.030 0.000 0.029 0.030 0.000
28 Escherichia/Shigella 0.008 0.000 0.008 0.008 0.000
30 F__Enterobacteriaceae -0.014 0.000 -0.015 -0.014 0.000
31 F__Erysipelotrichaceae 0.008 0.000 0.006 0.010 0.000
32 F__Lachnospiraceae 0.015 0.000 0.014 0.015 0.000
33 F__Ruminococcaceae -0.011 0.000 -0.014 -0.009 0.000
34 Finegoldia -0.033 0.000 -0.049 -0.017 0.000
35 Flavonifractor -0.013 0.000 -0.015 -0.011 0.000
36 Fusicatenibacter 0.177 0.000 0.173 0.180 0.000
37 Fusobacterium -0.161 0.000 -0.167 -0.154 0.000
38 Gemella -0.054 0.000 -0.060 -0.048 0.000
39 Granulicatella 0.021 0.000 0.013 0.029 0.000
40 Haemophilus 0.059 0.000 0.056 0.061 0.000
41 Hungatella 0.049 0.000 0.042 0.055 0.000
42 Intestinibacter 0.056 0.000 0.052 0.060 0.000
43 Klebsiella 0.016 0.000 0.013 0.020 0.000
44 Lactobacillus -0.009 0.000 -0.010 -0.008 0.000
45 Lactococcus 0.039 0.000 0.028 0.051 0.000
46 O__Clostridiales 0.090 0.000 0.062 0.117 0.000
47 Parabacteroides 0.009 0.000 0.008 0.010 0.000
48 Parasutterella -0.056 0.000 -0.062 -0.051 0.000
49 Prevotella 0.234 0.000 0.227 0.240 0.000
50 Pseudomonas 0.022 0.000 0.020 0.025 0.000
51 Raoultella -0.101 0.000 -0.107 -0.095 0.000
52 Robinsoniella 0.046 0.000 0.044 0.049 0.000
53 Romboutsia -0.015 0.000 -0.019 -0.011 0.000
54 Roseburia -0.005 0.000 -0.006 -0.004 0.000
55 Rothia -0.029 0.000 -0.035 -0.023 0.000
56 Ruminococcus 0.049 0.000 0.046 0.051 0.000
57 Ruminococcus2 -0.005 0.000 -0.006 -0.003 0.000
58 Staphylococcus 0.004 0.000 0.003 0.005 0.000
59 Streptococcus -0.050 0.000 -0.051 -0.050 0.000
60 Subdoligranulum -0.061 0.000 -0.065 -0.057 0.000
61 Sutterella -0.043 0.000 -0.047 -0.039 0.000
62 Terrisporobacter 0.126 0.000 0.118 0.134 0.000
63 Varibaculum 0.162 0.000 0.110 0.213 0.000
64 Veillonella 0.013 0.000 0.013 0.014 0.000
66 F__Peptostreptococcaceae 0.025 0.000 0.018 0.031 0.000
67 Oscillibacter -0.017 0.000 -0.025 -0.008 0.000
7 Anaerotruncus 0.023 0.001 0.010 0.037 0.001
29 Eubacterium -0.005 0.001 -0.008 -0.002 0.001
sessionInfo()R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] vegan_2.6-2 lattice_0.20-45 permute_0.9-7
loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 pillar_1.8.0 compiler_4.1.2 bslib_0.4.0
[5] later_1.3.0 jquerylib_0.1.4 git2r_0.30.1 highr_0.9
[9] workflowr_1.7.0 tools_4.1.2 digest_0.6.29 nlme_3.1-153
[13] jsonlite_1.8.0 evaluate_0.15 lifecycle_1.0.1 tibble_3.1.7
[17] mgcv_1.8-38 pkgconfig_2.0.3 rlang_1.0.4 Matrix_1.3-4
[21] cli_3.3.0 rstudioapi_0.13 parallel_4.1.2 yaml_2.3.5
[25] xfun_0.31 fastmap_1.1.0 cluster_2.1.2 stringr_1.4.0
[29] knitr_1.39 fs_1.5.2 vctrs_0.4.1 sass_0.4.2
[33] grid_4.1.2 rprojroot_2.0.3 glue_1.6.2 R6_2.5.1
[37] fansi_1.0.3 rmarkdown_2.14 magrittr_2.0.3 splines_4.1.2
[41] MASS_7.3-54 promises_1.2.0.1 ellipsis_0.3.2 htmltools_0.5.2
[45] httpuv_1.6.5 utf8_1.2.2 stringi_1.7.6 cachem_1.0.6