## ----getPackage, eval=FALSE------------------------------------------------ # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("dcanr") ## ---- eval = FALSE--------------------------------------------------------- # BiocManager::install("DavisLaboratory/dcanr") ## ----Load, message=FALSE--------------------------------------------------- library(dcanr) ## ----echo=TRUE, message=FALSE, warning=FALSE------------------------------- library(dcanr) dcMethods() ## -------------------------------------------------------------------------- #load data data(sim102) #get available conditions getConditionNames(sim102) #get expression data and conditions for 'UME6' knock-down simdata <- getSimData(sim102, cond.name = 'UME6', full = FALSE) emat <- simdata$emat ume6_kd <- simdata$condition print(emat[1:5, 1:5]) #149 genes and 406 samples head(ume6_kd) #NOTE: binary conditions encoded with 1's and 2's ## -------------------------------------------------------------------------- #apply the z-score method with Spearman correlations z_scores <- dcScore(emat, ume6_kd, dc.method = 'zscore', cor.method = 'spearman') print(z_scores[1:5, 1:5]) ## -------------------------------------------------------------------------- #perform a statistical test: the z-test is selected automatically raw_p <- dcTest(z_scores, emat, ume6_kd) print(raw_p[1:5, 1:5]) ## -------------------------------------------------------------------------- #adjust p-values (raw p-values from dcTest should NOT be modified) adj_p <- dcAdjust(raw_p, f = p.adjust, method = 'fdr') print(adj_p[1:5, 1:5]) ## ----message=FALSE, warning=FALSE, fig.wide=TRUE--------------------------- library(igraph) #get the differential network dcnet <- dcNetwork(z_scores, adj_p) plot(dcnet, vertex.label = '') #convert to an adjacency matrix adjmat <- as_adj(dcnet, sparse = FALSE) print(adjmat[1:5, 1:5]) #convert to a data.frame edgedf <- as_data_frame(dcnet, what = 'edges') print(head(edgedf)) ## ----sessionInfo, echo=FALSE----------------------------------------------- sessionInfo()