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Mediation_Analysis.R
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#Cleaning the data table All Samples----
library(mediation)
set.seed(1000)
m.otu <- Oct23_16S.056.a.micro2.c$otu_table
m.meta <- Oct23_16S.056.a.micro2.c$sample_table
m.taxa <- Oct23_16S.056.a.micro2.c$tax_table
m.taxa.abund <- Oct23_16S.056.a.micro2.c$taxa_abund
m.taxa.abund.genus <- m.taxa.abund$Genus
m.taxa.abund.species <- m.taxa.abund$Species
m.taxa.abund.genus <- as.data.frame(t(m.taxa.abund.genus))
m.taxa.abund.species <- as.data.frame(t(m.taxa.abund.species))
#merging metadata and taxa abundance table (not changing "label" genus)
m.genus <- cbind(m.meta, m.taxa.abund.species)
#replace - with space
m.genus$Age <- gsub("-", "", m.genus$Age, fixed = TRUE)
#replace - with space
m.genus$Semen_Volume <- gsub("-", "", m.genus$Semen_Volume, fixed = TRUE)
#Check Class for each column
m.class.check <- as.data.frame(sapply(m.genus, class))
#make numeric for Age
m.genus$Age <- as.numeric(m.genus$Age)
#make numeric for Normal Fertilization Rate
m.genus$Normal_Fertilization_Rate <- as.numeric(m.genus$Normal_Fertilization_Rate)
m.genus$Normal_Fertilization_Rate <- as.numeric(m.genus$Normal_Fertilization_Rate)
#make numeric for Semen Volume
m.genus$Semen_Volume <- as.numeric(m.genus$Semen_Volume)
#count number of NA
sum(is.na(m.genus))
#NA did not affect the Mediation lm and Outcome lm models, but affect
#the mediation analysis package
#omit patient with NA data
m.genus.o <- na.omit(m.genus)
sum(is.na(m.genus.o)) #omitted 9 patients' data
#When no. of cells that has a non-zero value is less than or equal to 1,
#the mediation analysis did not work
#so, need to remove the column that has
# " no. of cells that has a non-zero value is less than or equal to 1
sum(m.genus.o[,225] > 0) <= 1
#Check no. of cells that has a non-zero value is less than or equal to 1
#for @ column, similar as above
s <- as.data.frame(colSums(m.genus.o !=1))
##_________________________#####
#DEFB119 as Treatment###########
#Microbiome Analysis - Control Sample----
m.genus.o2 <- m.genus.o[which(m.genus.o$Fertility=='Control'),]
#removal of column which has 1 cells or less containing zero value
m.genus.o2 <- m.genus.o2[, colSums(m.genus.o2 !=0) >= 2]
##DEFB119 > Microbiome > SemenParameter-Forward----
m.vec <- NULL
for ( i in 17:38){
for ( j in 8:12){
Treat <- colnames(m.genus.o2)[13]
Mediator <- colnames(m.genus.o2)[i]
Outcome <- colnames(m.genus.o2)[j]
#Mediation lm: Microbiome > Defb119 >
med_formula = as.formula(paste('`',Mediator,'`', "~", '`',
Treat,'`', "+", "Age", sep = ""))
mediate_micro_def <- lm(med_formula, data=m.genus.o2)
###Outcome lm: Microbiome -> Semen parameters
out_formula = as.formula(paste('`',Outcome,'`', "~",
'`',Treat,'`', "+",'`', Mediator,'`', "+",
"Age", sep = ""))
out_micro_def <- lm(out_formula, data=m.genus.o2)
###Mediation- Med vs Out lm
results=mediate(mediate_micro_def, out_micro_def, treat=Treat,
mediator=Mediator,
robustSE = TRUE, boot=F, sims = 1000)
m.summary = (summary(results))
id <- paste("T:", Treat,">", "M:",Mediator,">",
"O:", Outcome, sep="")
m.res <- capture.output(m.summary,append=FALSE)
#sub( "^()\\s", "\\1", res[7]) grab ACME p value
tmp <- base::strsplit(m.res[grep("ACME",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T)] # remove stars in case the last element is star
m.ACME <- tmp[(2)]
tmp <- base::strsplit(m.res[grep("ACME",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T)] # remove stars in case the last element is star
m.ACME.p <- tmp[length(tmp)]
tmp <- base::strsplit(m.res[grep("ADE",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T)] # remove stars in case the last element is star
m.ADE <- tmp[(2)]
tmp <- base::strsplit(m.res[grep("ADE",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T) ] # remove stars in case the last element is star
m.ADE.p <- tmp[length(tmp)]
tmp <- base::strsplit(m.res[grep("Total Effect", m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" ]
tmp <- tmp[!grepl("*",tmp,fixed = T) ] # remove stars in case the last element is star
i_str = which(grepl("Effect", tmp))
m.totale <- tmp[(i_str + 1)]
tmp <- base::strsplit(m.res[grep("Total Effect", m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" ]
tmp <- tmp[!grepl("*",tmp,fixed = T) ] # remove stars in case the last element is star
m.totale.p <- tmp[length(tmp)]
tmp <- base::strsplit(m.res[grep("Prop. Mediated", m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" ]
i_str = which(grepl("Mediated", tmp))
m.prop.mediated <- tmp[(i_str + 1)]
m.vec.a = c(id, m.ACME, m.ACME.p, m.ADE, m.ADE.p, m.totale, m.totale.p, m.prop.mediated)
names(m.vec.a) <- c("Treat_Mediator_Outcome", "ACME", "ACME.p", "ADE", "ADE.p", "Total.Effect",
"Total.Effect.p", "prop.mediated")
#Glue data together
m.vec = rbind(m.vec, m.vec.a)
}}
library(writexl)
m.vec.con_def_Micro_sem_f <- as.data.frame(m.vec)
write_xlsx(m.vec.con_def_Micro_sem_f,
"DEFB119_Micro_Sem_Con_For.xlsx")
##DEFB119 > SemenParameter > Microbiome-Reverse----
m.vec <- NULL
for ( i in 8:12){
for ( j in 17:38){
Treat <- colnames(m.genus.o2)[13]
Mediator <- colnames(m.genus.o2)[i]
Outcome <- colnames(m.genus.o2)[j]
#Mediation lm: Microbiome > Defb119 >
med_formula = as.formula(paste('`',Mediator,'`', "~", '`',
Treat,'`', "+", "Age", sep = ""))
mediate_micro_def <- lm(med_formula, data=m.genus.o2)
###Outcome lm: Microbiome -> Semen parameters
out_formula = as.formula(paste('`',Outcome,'`', "~",
'`',Treat,'`', "+",'`', Mediator,'`', "+",
"Age", sep = ""))
out_micro_def <- lm(out_formula, data=m.genus.o2)
###Mediation- Med vs Out lm
results=mediate(mediate_micro_def, out_micro_def, treat=Treat,
mediator=Mediator,
robustSE = TRUE, boot=F, sims = 1000)
m.summary = (summary(results))
id <- paste("T:", Treat,">", "M:",Mediator,">",
"O:", Outcome, sep="")
m.res <- capture.output(m.summary,append=FALSE)
#sub( "^()\\s", "\\1", res[7]) grab ACME p value
tmp <- base::strsplit(m.res[grep("ACME",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T)] # remove stars in case the last element is star
m.ACME <- tmp[(2)]
tmp <- base::strsplit(m.res[grep("ACME",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T)] # remove stars in case the last element is star
m.ACME.p <- tmp[length(tmp)]
tmp <- base::strsplit(m.res[grep("ADE",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T)] # remove stars in case the last element is star
m.ADE <- tmp[(2)]
tmp <- base::strsplit(m.res[grep("ADE",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T) ] # remove stars in case the last element is star
m.ADE.p <- tmp[length(tmp)]
tmp <- base::strsplit(m.res[grep("Total Effect", m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" ]
tmp <- tmp[!grepl("*",tmp,fixed = T) ] # remove stars in case the last element is star
i_str = which(grepl("Effect", tmp))
m.totale <- tmp[(i_str + 1)]
tmp <- base::strsplit(m.res[grep("Total Effect", m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" ]
tmp <- tmp[!grepl("*",tmp,fixed = T) ] # remove stars in case the last element is star
m.totale.p <- tmp[length(tmp)]
tmp <- base::strsplit(m.res[grep("Prop. Mediated", m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" ]
i_str = which(grepl("Mediated", tmp))
m.prop.mediated <- tmp[(i_str + 1)]
m.vec.a = c(id, m.ACME, m.ACME.p, m.ADE, m.ADE.p, m.totale, m.totale.p, m.prop.mediated)
names(m.vec.a) <- c("Treat_Mediator_Outcome", "ACME", "ACME.p", "ADE", "ADE.p", "Total.Effect",
"Total.Effect.p", "prop.mediated")
#Glue data together
m.vec = rbind(m.vec, m.vec.a)
}}
library(writexl)
m.vec.con_def_Micro_sem_r <- as.data.frame(m.vec)
write_xlsx(m.vec.con_def_Micro_sem_r,
"DEFB119_Micro_Sem_Con_Rev.xlsx")
###############################
###############################
#Microbiome Analysis - Infertile Sample----
m.genus.o2 <- m.genus.o[which(m.genus.o$Fertility=='Infertile'),]
#removal of column which has 1 cells or less containing zero value
m.genus.o2 <- m.genus.o2[, colSums(m.genus.o2 !=0) >= 2]
##DEFB119 > Microbiome > SemenParameter-Forward----
m.vec <- NULL
for ( i in 17:38){
for ( j in 8:12){
Treat <- colnames(m.genus.o2)[13]
Mediator <- colnames(m.genus.o2)[i]
Outcome <- colnames(m.genus.o2)[j]
#Mediation lm: Microbiome > Defb119 >
med_formula = as.formula(paste('`',Mediator,'`', "~", '`',
Treat,'`', "+", "Age", sep = ""))
mediate_micro_def <- lm(med_formula, data=m.genus.o2)
###Outcome lm: Microbiome -> Semen parameters
out_formula = as.formula(paste('`',Outcome,'`', "~",
'`',Treat,'`', "+",'`', Mediator,'`', "+",
"Age", sep = ""))
out_micro_def <- lm(out_formula, data=m.genus.o2)
###Mediation- Med vs Out lm
results=mediate(mediate_micro_def, out_micro_def, treat=Treat,
mediator=Mediator,
robustSE = TRUE, boot=F, sims = 1000)
m.summary = (summary(results))
id <- paste("T:", Treat,">", "M:",Mediator,">",
"O:", Outcome, sep="")
m.res <- capture.output(m.summary,append=FALSE)
#sub( "^()\\s", "\\1", res[7]) grab ACME p value
tmp <- base::strsplit(m.res[grep("ACME",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T)] # remove stars in case the last element is star
m.ACME <- tmp[(2)]
tmp <- base::strsplit(m.res[grep("ACME",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T)] # remove stars in case the last element is star
m.ACME.p <- tmp[length(tmp)]
tmp <- base::strsplit(m.res[grep("ADE",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T)] # remove stars in case the last element is star
m.ADE <- tmp[(2)]
tmp <- base::strsplit(m.res[grep("ADE",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T) ] # remove stars in case the last element is star
m.ADE.p <- tmp[length(tmp)]
tmp <- base::strsplit(m.res[grep("Total Effect", m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" ]
tmp <- tmp[!grepl("*",tmp,fixed = T) ] # remove stars in case the last element is star
i_str = which(grepl("Effect", tmp))
m.totale <- tmp[(i_str + 1)]
tmp <- base::strsplit(m.res[grep("Total Effect", m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" ]
tmp <- tmp[!grepl("*",tmp,fixed = T) ] # remove stars in case the last element is star
m.totale.p <- tmp[length(tmp)]
tmp <- base::strsplit(m.res[grep("Prop. Mediated", m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" ]
i_str = which(grepl("Mediated", tmp))
m.prop.mediated <- tmp[(i_str + 1)]
m.vec.a = c(id, m.ACME, m.ACME.p, m.ADE, m.ADE.p, m.totale, m.totale.p, m.prop.mediated)
names(m.vec.a) <- c("Treat_Mediator_Outcome", "ACME", "ACME.p", "ADE", "ADE.p", "Total.Effect",
"Total.Effect.p", "prop.mediated")
#Glue data together
m.vec = rbind(m.vec, m.vec.a)
}}
library(writexl)
m.vec.In_def_Micro_sem_f <- as.data.frame(m.vec)
write_xlsx(m.vec.In_def_Micro_sem_f,
"DEFB119_Micro_Sem_In_For.xlsx")
##DEFB119 > SemenParameter > Microbiome-Reverse----
m.vec <- NULL
for ( i in 8:12){
for ( j in 17:38){
Treat <- colnames(m.genus.o2)[13]
Mediator <- colnames(m.genus.o2)[i]
Outcome <- colnames(m.genus.o2)[j]
#Mediation lm: Microbiome > Defb119 >
med_formula = as.formula(paste('`',Mediator,'`', "~", '`',
Treat,'`', "+", "Age", sep = ""))
mediate_micro_def <- lm(med_formula, data=m.genus.o2)
###Outcome lm: Microbiome -> Semen parameters
out_formula = as.formula(paste('`',Outcome,'`', "~",
'`',Treat,'`', "+",'`', Mediator,'`', "+",
"Age", sep = ""))
out_micro_def <- lm(out_formula, data=m.genus.o2)
###Mediation- Med vs Out lm
results=mediate(mediate_micro_def, out_micro_def, treat=Treat,
mediator=Mediator,
robustSE = TRUE, boot=F, sims = 1000)
m.summary = (summary(results))
id <- paste("T:", Treat,">", "M:",Mediator,">",
"O:", Outcome, sep="")
m.res <- capture.output(m.summary,append=FALSE)
#sub( "^()\\s", "\\1", res[7]) grab ACME p value
tmp <- base::strsplit(m.res[grep("ACME",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T)] # remove stars in case the last element is star
m.ACME <- tmp[(2)]
tmp <- base::strsplit(m.res[grep("ACME",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T)] # remove stars in case the last element is star
m.ACME.p <- tmp[length(tmp)]
tmp <- base::strsplit(m.res[grep("ADE",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T)] # remove stars in case the last element is star
m.ADE <- tmp[(2)]
tmp <- base::strsplit(m.res[grep("ADE",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T) ] # remove stars in case the last element is star
m.ADE.p <- tmp[length(tmp)]
tmp <- base::strsplit(m.res[grep("Total Effect", m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" ]
tmp <- tmp[!grepl("*",tmp,fixed = T) ] # remove stars in case the last element is star
i_str = which(grepl("Effect", tmp))
m.totale <- tmp[(i_str + 1)]
tmp <- base::strsplit(m.res[grep("Total Effect", m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" ]
tmp <- tmp[!grepl("*",tmp,fixed = T) ] # remove stars in case the last element is star
m.totale.p <- tmp[length(tmp)]
tmp <- base::strsplit(m.res[grep("Prop. Mediated", m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" ]
i_str = which(grepl("Mediated", tmp))
m.prop.mediated <- tmp[(i_str + 1)]
m.vec.a = c(id, m.ACME, m.ACME.p, m.ADE, m.ADE.p, m.totale, m.totale.p, m.prop.mediated)
names(m.vec.a) <- c("Treat_Mediator_Outcome", "ACME", "ACME.p", "ADE", "ADE.p", "Total.Effect",
"Total.Effect.p", "prop.mediated")
#Glue data together
m.vec = rbind(m.vec, m.vec.a)
}}
library(writexl)
m.vec.In_def_Micro_sem_r <- as.data.frame(m.vec)
write_xlsx(m.vec.In_def_Micro_sem_r,
"DEFB119_Micro_Sem_In_Rev.xlsx")
##_________________________#####
#Microbiome as Treatment###########
##Control Sample----
m.genus.o2 <- m.genus.o[which(m.genus.o$Fertility=='Control'),]
#removal of column which has 1 cells or less containing zero value
m.genus.o2 <- m.genus.o2[, colSums(m.genus.o2 !=0) >= 2]
###Microbiome > Defb119 > SemenParameter-Forward----
m.vec <- NULL
for ( i in 17:38){
for ( j in 8:12){
Treat <- colnames(m.genus.o2)[i]
Mediator <- colnames(m.genus.o2)[13]
Outcome <- colnames(m.genus.o2)[j]
#Mediation lm: Microbiome > Defb119 >
med_formula = as.formula(paste('`',Mediator,'`', "~", '`',
Treat,'`', "+", "Age", sep = ""))
mediate_micro_def <- lm(med_formula, data=m.genus.o2)
###Outcome lm: Microbiome -> Semen parameters
out_formula = as.formula(paste('`',Outcome,'`', "~",
'`',Treat,'`', "+",'`', Mediator,'`', "+",
"Age", sep = ""))
out_micro_def <- lm(out_formula, data=m.genus.o2)
###Mediation- Med vs Out lm
results=mediate(mediate_micro_def, out_micro_def, treat=Treat,
mediator=Mediator,
robustSE = TRUE, boot=F, sims = 1000)
m.summary = (summary(results))
id <- paste("T:", Treat,">", "M:",Mediator,">",
"O:", Outcome, sep="")
m.res <- capture.output(m.summary,append=FALSE)
#sub( "^()\\s", "\\1", res[7]) grab ACME p value
tmp <- base::strsplit(m.res[grep("ACME",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T)] # remove stars in case the last element is star
m.ACME <- tmp[(2)]
tmp <- base::strsplit(m.res[grep("ACME",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T)] # remove stars in case the last element is star
m.ACME.p <- tmp[length(tmp)]
tmp <- base::strsplit(m.res[grep("ADE",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T)] # remove stars in case the last element is star
m.ADE <- tmp[(2)]
tmp <- base::strsplit(m.res[grep("ADE",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T) ] # remove stars in case the last element is star
m.ADE.p <- tmp[length(tmp)]
tmp <- base::strsplit(m.res[grep("Total Effect", m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" ]
tmp <- tmp[!grepl("*",tmp,fixed = T) ] # remove stars in case the last element is star
i_str = which(grepl("Effect", tmp))
m.totale <- tmp[(i_str + 1)]
tmp <- base::strsplit(m.res[grep("Total Effect", m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" ]
tmp <- tmp[!grepl("*",tmp,fixed = T) ] # remove stars in case the last element is star
m.totale.p <- tmp[length(tmp)]
tmp <- base::strsplit(m.res[grep("Prop. Mediated", m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" ]
i_str = which(grepl("Mediated", tmp))
m.prop.mediated <- tmp[(i_str + 1)]
m.vec.a = c(id, m.ACME, m.ACME.p, m.ADE, m.ADE.p, m.totale, m.totale.p, m.prop.mediated)
names(m.vec.a) <- c("Treat_Mediator_Outcome", "ACME", "ACME.p", "ADE", "ADE.p", "Total.Effect",
"Total.Effect.p", "prop.mediated")
#Glue data together
m.vec = rbind(m.vec, m.vec.a)
}}
library(writexl)
m.vec.con_micro_def_sem_f <- as.data.frame(m.vec)
write_xlsx(m.vec.con_micro_def_sem_f,
"Micro_DEFB119_Semen_Con_For.xlsx")
###Microbiome > SemenParameter > DEFB119 -Rev----
m.vec <- NULL
for ( i in 17:38){
for ( j in 8:12){
Treat <- colnames(m.genus.o2)[i]
Mediator <- colnames(m.genus.o2)[j]
Outcome <- colnames(m.genus.o2)[13]
#Mediation lm: Microbiome > Defb119 >
med_formula = as.formula(paste('`',Mediator,'`', "~", '`',
Treat,'`', "+", "Age", sep = ""))
mediate_micro_def <- lm(med_formula, data=m.genus.o2)
###Outcome lm: Microbiome -> Semen parameters
out_formula = as.formula(paste('`',Outcome,'`', "~",
'`',Treat,'`', "+",'`', Mediator,'`', "+",
"Age", sep = ""))
out_micro_def <- lm(out_formula, data=m.genus.o2)
###Mediation- Med vs Out lm
results=mediate(mediate_micro_def, out_micro_def, treat=Treat,
mediator=Mediator,
robustSE = TRUE, boot=F, sims = 1000)
m.summary = (summary(results))
id <- paste("T:", Treat,">", "M:",Mediator,">",
"O:", Outcome, sep="")
m.res <- capture.output(m.summary,append=FALSE)
#sub( "^()\\s", "\\1", res[7]) grab ACME p value
tmp <- base::strsplit(m.res[grep("ACME",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T)] # remove stars in case the last element is star
m.ACME <- tmp[(2)]
tmp <- base::strsplit(m.res[grep("ACME",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T)] # remove stars in case the last element is star
m.ACME.p <- tmp[length(tmp)]
tmp <- base::strsplit(m.res[grep("ADE",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T)] # remove stars in case the last element is star
m.ADE <- tmp[(2)]
tmp <- base::strsplit(m.res[grep("ADE",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T) ] # remove stars in case the last element is star
m.ADE.p <- tmp[length(tmp)]
tmp <- base::strsplit(m.res[grep("Total Effect", m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" ]
tmp <- tmp[!grepl("*",tmp,fixed = T) ] # remove stars in case the last element is star
i_str = which(grepl("Effect", tmp))
m.totale <- tmp[(i_str + 1)]
tmp <- base::strsplit(m.res[grep("Total Effect", m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" ]
tmp <- tmp[!grepl("*",tmp,fixed = T) ] # remove stars in case the last element is star
m.totale.p <- tmp[length(tmp)]
tmp <- base::strsplit(m.res[grep("Prop. Mediated", m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" ]
i_str = which(grepl("Mediated", tmp))
m.prop.mediated <- tmp[(i_str + 1)]
m.vec.a = c(id, m.ACME, m.ACME.p, m.ADE, m.ADE.p, m.totale, m.totale.p, m.prop.mediated)
names(m.vec.a) <- c("Treat_Mediator_Outcome", "ACME", "ACME.p", "ADE", "ADE.p", "Total.Effect",
"Total.Effect.p", "prop.mediated")
#Glue data together
m.vec = rbind(m.vec, m.vec.a)
}}
library(writexl)
m.vec.con_micro_def_sem_r <- as.data.frame(m.vec)
write_xlsx(m.vec.con_micro_def_sem_r,
"Micro_DEFB119_Semen_Con_Rev.xlsx")
##Infertile Sample----
m.genus.o2 <- m.genus.o[which(m.genus.o$Fertility=='Infertile'),]
#removal of column which has 1 cells or less containing zero value
m.genus.o2 <- m.genus.o2[, colSums(m.genus.o2 !=0) >= 2]
###Microbiome > Defb119 > SemenParameter-Forward----
m.vec <- NULL
for ( i in 17:38){
for ( j in 8:12){
Treat <- colnames(m.genus.o2)[i]
Mediator <- colnames(m.genus.o2)[13]
Outcome <- colnames(m.genus.o2)[j]
#Mediation lm: Microbiome > Defb119 >
med_formula = as.formula(paste('`',Mediator,'`', "~", '`',
Treat,'`', "+", "Age", sep = ""))
mediate_micro_def <- lm(med_formula, data=m.genus.o2)
###Outcome lm: Microbiome -> Semen parameters
out_formula = as.formula(paste('`',Outcome,'`', "~",
'`',Treat,'`', "+",'`', Mediator,'`', "+",
"Age", sep = ""))
out_micro_def <- lm(out_formula, data=m.genus.o2)
###Mediation- Med vs Out lm
results=mediate(mediate_micro_def, out_micro_def, treat=Treat,
mediator=Mediator,
robustSE = TRUE, boot=F, sims = 1000)
m.summary = (summary(results))
id <- paste("T:", Treat,">", "M:",Mediator,">",
"O:", Outcome, sep="")
m.res <- capture.output(m.summary,append=FALSE)
#sub( "^()\\s", "\\1", res[7]) grab ACME p value
tmp <- base::strsplit(m.res[grep("ACME",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T)] # remove stars in case the last element is star
m.ACME <- tmp[(2)]
tmp <- base::strsplit(m.res[grep("ACME",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T)] # remove stars in case the last element is star
m.ACME.p <- tmp[length(tmp)]
tmp <- base::strsplit(m.res[grep("ADE",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T)] # remove stars in case the last element is star
m.ADE <- tmp[(2)]
tmp <- base::strsplit(m.res[grep("ADE",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T) ] # remove stars in case the last element is star
m.ADE.p <- tmp[length(tmp)]
tmp <- base::strsplit(m.res[grep("Total Effect", m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" ]
tmp <- tmp[!grepl("*",tmp,fixed = T) ] # remove stars in case the last element is star
i_str = which(grepl("Effect", tmp))
m.totale <- tmp[(i_str + 1)]
tmp <- base::strsplit(m.res[grep("Total Effect", m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" ]
tmp <- tmp[!grepl("*",tmp,fixed = T) ] # remove stars in case the last element is star
m.totale.p <- tmp[length(tmp)]
tmp <- base::strsplit(m.res[grep("Prop. Mediated", m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" ]
i_str = which(grepl("Mediated", tmp))
m.prop.mediated <- tmp[(i_str + 1)]
m.vec.a = c(id, m.ACME, m.ACME.p, m.ADE, m.ADE.p, m.totale, m.totale.p, m.prop.mediated)
names(m.vec.a) <- c("Treat_Mediator_Outcome", "ACME", "ACME.p", "ADE", "ADE.p", "Total.Effect",
"Total.Effect.p", "prop.mediated")
#Glue data together
m.vec = rbind(m.vec, m.vec.a)
}}
library(writexl)
m.vec.In_micro_def_sem_f <- as.data.frame(m.vec)
write_xlsx(m.vec.In_micro_def_sem_f,
"Micro_DEFB119_Semen_In_For.xlsx")
###Microbiome > SemenParameter > DEFB119 -Rev----
m.vec <- NULL
for ( i in 17:38){
for ( j in 8:12){
Treat <- colnames(m.genus.o2)[i]
Mediator <- colnames(m.genus.o2)[j]
Outcome <- colnames(m.genus.o2)[13]
#Mediation lm: Microbiome > Defb119 >
med_formula = as.formula(paste('`',Mediator,'`', "~", '`',
Treat,'`', "+", "Age", sep = ""))
mediate_micro_def <- lm(med_formula, data=m.genus.o2)
###Outcome lm: Microbiome -> Semen parameters
out_formula = as.formula(paste('`',Outcome,'`', "~",
'`',Treat,'`', "+",'`', Mediator,'`', "+",
"Age", sep = ""))
out_micro_def <- lm(out_formula, data=m.genus.o2)
###Mediation- Med vs Out lm
results=mediate(mediate_micro_def, out_micro_def, treat=Treat,
mediator=Mediator,
robustSE = TRUE, boot=F, sims = 1000)
m.summary = (summary(results))
id <- paste("T:", Treat,">", "M:",Mediator,">",
"O:", Outcome, sep="")
m.res <- capture.output(m.summary,append=FALSE)
#sub( "^()\\s", "\\1", res[7]) grab ACME p value
tmp <- base::strsplit(m.res[grep("ACME",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T)] # remove stars in case the last element is star
m.ACME <- tmp[(2)]
tmp <- base::strsplit(m.res[grep("ACME",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T)] # remove stars in case the last element is star
m.ACME.p <- tmp[length(tmp)]
tmp <- base::strsplit(m.res[grep("ADE",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T)] # remove stars in case the last element is star
m.ADE <- tmp[(2)]
tmp <- base::strsplit(m.res[grep("ADE",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T) ] # remove stars in case the last element is star
m.ADE.p <- tmp[length(tmp)]
tmp <- base::strsplit(m.res[grep("Total Effect", m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" ]
tmp <- tmp[!grepl("*",tmp,fixed = T) ] # remove stars in case the last element is star
i_str = which(grepl("Effect", tmp))
m.totale <- tmp[(i_str + 1)]
tmp <- base::strsplit(m.res[grep("Total Effect", m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" ]
tmp <- tmp[!grepl("*",tmp,fixed = T) ] # remove stars in case the last element is star
m.totale.p <- tmp[length(tmp)]
tmp <- base::strsplit(m.res[grep("Prop. Mediated", m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" ]
i_str = which(grepl("Mediated", tmp))
m.prop.mediated <- tmp[(i_str + 1)]
m.vec.a = c(id, m.ACME, m.ACME.p, m.ADE, m.ADE.p, m.totale, m.totale.p, m.prop.mediated)
names(m.vec.a) <- c("Treat_Mediator_Outcome", "ACME", "ACME.p", "ADE", "ADE.p", "Total.Effect",
"Total.Effect.p", "prop.mediated")
#Glue data together
m.vec = rbind(m.vec, m.vec.a)
}}
library(writexl)
m.vec.In_micro_def_sem_r <- as.data.frame(m.vec)
write_xlsx(m.vec.In_micro_def_sem_r,
"Micro_DEFB119_Semen_In_Rev.xlsx")
###________________________########
#SemenParameter as Treatment###########
##Control Sample----
m.genus.o2 <- m.genus.o[which(m.genus.o$Fertility=='Control'),]
#removal of column which has 1 cells or less containing zero value
m.genus.o2 <- m.genus.o2[, colSums(m.genus.o2 !=0) >= 2]
###Semen Parameter > DEFB119 > Microbiome -Forward----
m.vec <- NULL
for ( i in 8:12){
for ( j in 17:38){
Treat <- colnames(m.genus.o2)[i]
Mediator <- colnames(m.genus.o2)[13]
Outcome <- colnames(m.genus.o2)[j]
#Mediation lm: SemenParameter > Microbiome
med_formula = as.formula(paste('`',Mediator,'`', "~", '`',
Treat,'`', "+", "Age", sep = ""))
mediate_micro_def <- lm(med_formula, data=m.genus.o2)
###Outcome lm: SemenParameter -> DEFB119
out_formula = as.formula(paste('`',Outcome,'`', "~",
'`',Treat,'`', "+",'`', Mediator,'`', "+",
"Age", sep = ""))
out_micro_def <- lm(out_formula, data=m.genus.o2)
###Mediation- Med vs Out lm
results=mediate(mediate_micro_def, out_micro_def, treat=Treat,
mediator=Mediator,
robustSE = TRUE, boot=F, sims = 1000)
m.summary = (summary(results))
id <- paste("T:", Treat,">", "M:",Mediator,">",
"O:", Outcome, sep="")
m.res <- capture.output(m.summary,append=FALSE)
#sub( "^()\\s", "\\1", res[7]) grab ACME p value
tmp <- base::strsplit(m.res[grep("ACME",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T)] # remove stars in case the last element is star
m.ACME <- tmp[(2)]
tmp <- base::strsplit(m.res[grep("ACME",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T)] # remove stars in case the last element is star
m.ACME.p <- tmp[length(tmp)]
tmp <- base::strsplit(m.res[grep("ADE",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T)] # remove stars in case the last element is star
m.ADE <- tmp[(2)]
tmp <- base::strsplit(m.res[grep("ADE",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T) ] # remove stars in case the last element is star
m.ADE.p <- tmp[length(tmp)]
tmp <- base::strsplit(m.res[grep("Total Effect", m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" ]
tmp <- tmp[!grepl("*",tmp,fixed = T) ] # remove stars in case the last element is star
i_str = which(grepl("Effect", tmp))
m.totale <- tmp[(i_str + 1)]
tmp <- base::strsplit(m.res[grep("Total Effect", m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" ]
tmp <- tmp[!grepl("*",tmp,fixed = T) ] # remove stars in case the last element is star
m.totale.p <- tmp[length(tmp)]
tmp <- base::strsplit(m.res[grep("Prop. Mediated", m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" ]
i_str = which(grepl("Mediated", tmp))
m.prop.mediated <- tmp[(i_str + 1)]
m.vec.a = c(id, m.ACME, m.ACME.p, m.ADE, m.ADE.p, m.totale, m.totale.p, m.prop.mediated)
names(m.vec.a) <- c("Treat_Mediator_Outcome", "ACME", "ACME.p", "ADE", "ADE.p", "Total.Effect",
"Total.Effect.p", "prop.mediated")
#Glue data together
m.vec = rbind(m.vec, m.vec.a)
}}
library(writexl)
m.vec.con_sem_def_micro_f <- as.data.frame(m.vec)
write_xlsx(m.vec.con_sem_def_micro_f,
"Semen_DEFB119_Micro_Con_For.xlsx")
###SemenParameter > Microbiome > DEFB119-Rev----
m.vec <- NULL
for ( i in 8:12){
for ( j in 17:38){
Treat <- colnames(m.genus.o2)[i]
Mediator <- colnames(m.genus.o2)[j]
Outcome <- colnames(m.genus.o2)[13]
#Mediation lm: SemenParameter > Microbiome
med_formula = as.formula(paste('`',Mediator,'`', "~", '`',
Treat,'`', "+", "Age", sep = ""))
mediate_micro_def <- lm(med_formula, data=m.genus.o2)
###Outcome lm: SemenParameter -> DEFB119
out_formula = as.formula(paste('`',Outcome,'`', "~",
'`',Treat,'`', "+",'`', Mediator,'`', "+",
"Age", sep = ""))
out_micro_def <- lm(out_formula, data=m.genus.o2)
###Mediation- Med vs Out lm
results=mediate(mediate_micro_def, out_micro_def, treat=Treat,
mediator=Mediator,
robustSE = TRUE, boot=F, sims = 1000)
m.summary = (summary(results))
id <- paste("T:", Treat,">", "M:",Mediator,">",
"O:", Outcome, sep="")
m.res <- capture.output(m.summary,append=FALSE)
#sub( "^()\\s", "\\1", res[7]) grab ACME p value
tmp <- base::strsplit(m.res[grep("ACME",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T)] # remove stars in case the last element is star
m.ACME <- tmp[(2)]
tmp <- base::strsplit(m.res[grep("ACME",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T)] # remove stars in case the last element is star
m.ACME.p <- tmp[length(tmp)]
tmp <- base::strsplit(m.res[grep("ADE",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T)] # remove stars in case the last element is star
m.ADE <- tmp[(2)]
tmp <- base::strsplit(m.res[grep("ADE",m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" & tmp!="."]
tmp <- tmp[!grepl("*",tmp,fixed = T) ] # remove stars in case the last element is star
m.ADE.p <- tmp[length(tmp)]
tmp <- base::strsplit(m.res[grep("Total Effect", m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" ]
tmp <- tmp[!grepl("*",tmp,fixed = T) ] # remove stars in case the last element is star
i_str = which(grepl("Effect", tmp))
m.totale <- tmp[(i_str + 1)]
tmp <- base::strsplit(m.res[grep("Total Effect", m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" ]
tmp <- tmp[!grepl("*",tmp,fixed = T) ] # remove stars in case the last element is star
m.totale.p <- tmp[length(tmp)]
tmp <- base::strsplit(m.res[grep("Prop. Mediated", m.res)],"\\s")[[1]]
tmp <- tmp[tmp != "" ]
i_str = which(grepl("Mediated", tmp))