if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install() BiocManager::version() BiocManager::install("remotes", dependencies = TRUE) BiocManager::install("waldronlab/bugSigSimple")
Load bugSigSimple and bugSigDB
#library(bugSigDB) library (bugSigSimple)
dat <- bugsigdbr::importBugSigDB() dim(dat)
my.dat <- subsetByCurator(dat, curator="Fatima Zohra") table(my.dat[,"Condition"]) condsnew <-c("bipolar disorder","unipolar depression") condsnew <-c("bipolar disorder") efo <- bugsigdbr::getOntology("efo") dat.bpd <- bugsigdbr::subsetByOntology(dat, column = "Condition", "bipolar disorder", efo) dat.upd <- bugsigdbr::subsetByOntology(dat, column = "Condition", "unipolar depression", efo) my.dat.cond <- rbind(dat.bpd, dat.upd) table(my.dat.cond[,"Condition"])
getMostFrequentTaxa(my.dat.cond,n=30) getMostFrequentTaxa(my.dat.cond,, direction="UP") getMostFrequentTaxa(my.dat.cond,, direction="DOWN")
binom.test(x=4, n=6) binom.test(x=4, n=4) binom.test(x=4, n=4) binom.test(x=4, n=5) binom.test(x=4, n=5) binom.test(x=3, n=4) binom.test(x=3, n=5) binom.test(x=3, n=3) binom.test(x=3, n=3) binom.test(x=3, n=4)
binom.test(x=7, n=8) binom.test(x=6, n=6) binom.test(x=4, n=5) binom.test(x=4, n=5) binom.test(x=3, n=5) binom.test(x=3, n=5) binom.test(x=2, n=6) binom.test(x=2, n=2) binom.test(x=2, n=3) binom.test(x=2, n=2)
pvals <- c(0.6875, 0.125, 0.375, 0.625, 1, 0.25, 0.07031, 0.03125, 0.6875, 0.5) adj.pvals <- p.adjust(pvals, method="bonferroni") adj.pvals
ind <- my.dat.cond[,"Condition"] %in% c("bipolar disorder") my.dat.mdd <- my.dat.cond[!ind,] dim(my.dat.mdd) table(my.dat.mdd[,"Condition"]) getMostFrequentTaxa(my.dat.mdd, n=20) getMostFrequentTaxa(my.dat.mdd,sig.type= "increased") getMostFrequentTaxa(my.dat.mdd,sig.type= "decreased")
binom.test(x=3, n=3) binom.test(x=3, n=3) binom.test(x=3, n=4) binom.test(x=2, n=4) binom.test(x=2, n=3) binom.test(x=2, n=2) binom.test(x=2, n=4) binom.test(x=2, n=3) binom.test(x=2, n=4) binom.test(x=2, n=2)
binom.test(x=4, n=5) binom.test(x=4, n=4) binom.test(x=4, n=5) binom.test(x=3, n=5) binom.test(x=2, n=4) binom.test(x=2, n=4) binom.test(x=2, n=4) binom.test(x=2, n=4) binom.test(x=2, n=2) binom.test(x=2, n=2)
pvals <- c(0.6875, 0.125, 0.375, 0.625, 1, 0.25, 0.07031, 0.03125, 0.6875, 0.5) adj.pvals <- p.adjust(pvals, method="fdr") adj.pvals
ind <- my.dat.cond[,"Condition"] %in% c("unipolar depression") my.dat.bd <- my.dat.cond[!ind,] dim(my.dat.bd) table(my.dat.bd[,"Condition"]) getMostFrequentTaxa(my.dat.bd, n=20) getMostFrequentTaxa(my.dat.bd,, direction="UP") getMostFrequentTaxa(my.dat.bd,, direction="DOWN")
binom.test(x=4, n=4) binom.test(x=4, n=4) binom.test(x=4, n=4) binom.test(x=2, n=2) binom.test(x=2, n=2) binom.test(x=2, n=2) binom.test(x=2, n=3) binom.test(x=1, n=2)
binom.test(x=4, n=5) binom.test(x=4, n=4) binom.test(x=4, n=5) binom.test(x=3, n=5) binom.test(x=2, n=4) binom.test(x=2, n=4) binom.test(x=2, n=4) binom.test(x=2, n=4) binom.test(x=2, n=2) binom.test(x=2, n=2)
taxa.mdd <- c(up=1/7, down=4/7) taxa.bd <- c(up=0/4, down=3/4) barplot(rbind(taxa.mdd, taxa.bd), beside=TRUE, col=c("red","blue"), legend=TRUE, args.legend=list(x="topleft", legend=c("major depressive disorder", "bipolar disorder")), ylab="relative frequency", main="Frequency of Faecalibacterium")
taxa.mdd <- c(up=2/7, down=2/7) taxa.bd <- c(up=2/4, down=0/4) barplot(rbind(taxa.mdd, taxa.bd), beside=TRUE, col=c("red","blue"), legend=TRUE, args.legend=list(x="topright", cex = 0.70, legend=c("major depressive disorder", "bipolar disorder")), ylab="relative frequency", main="Frequency of Actinobacteria")
taxa.mdd <- c(up=2/7, down=2/7) taxa.bd <- c(up=0/4, down=2/4) barplot(rbind(taxa.mdd, taxa.bd), beside=TRUE, col=c("red","blue"), legend=TRUE, args.legend=list(x="topleft", cex = 0.80, legend=c("major depressive disorder", "bipolar disorder")), ylab="relative frequency", main="Frequency of Bacteroides")
taxa.mdd <- c(up=0/7, down=4/7) taxa.bd <- c(up=0/4, down=2/4) barplot(rbind(taxa.mdd, taxa.bd), beside=TRUE, col=c("red","blue"), legend=TRUE, args.legend=list(x="topleft", cex = 0.75, legend=c("major depressive disorder", "bipolar disorder")), ylab="relative frequency", main="Frequency of Ruminococcaceae")
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