# Draw the Manhattan plot. The function metaGE.manhattan displays the Manhattan plot of the -log10(p-value) or the local score of each marker along the genome. ```r metaGE.manhattan( Data, VarName, Threshold = NULL, SigZones = NULL, Score = FALSE, AnnotateMarkers = NULL, Main = "", col = c("grey", "black"), colSigZones = "blue", Ylim = NULL ) ``` ## Arguments - `Data`: A dataset containing the columns: CHR, POS, MARKER and the variable to plot for each marker, as obtained from `metaGE.fit()`. - `VarName`: The name of the column containing the variable to plot, generally the p-value or a score. - `Threshold`: A threshold in order to draw a "genome-wide significant" line. (optional) - `SigZones`: A dataset containing the significant zones to plot, as obtained from `metaGE.lscore()`. Must have columns: CHR, Start, End. (optional) - `Score`: A boolean. If `FALSE`, the -log10 of the variable is plotted, useful for plotting p-values. If `TRUE`, the raw values of the variable is plotted, useful for plotting scores. (`FALSE` by default) - `AnnotateMarkers`: A list of markers name to annotate in the plot. (optional) - `Main`: The main to display. (optional) - `col`: A character vector indicating which colors to alternate for different chromosomes. (optional) - `colSigZones`: A character indicating which color to plot the significant zones.("`blue`" by default) - `Ylim`: Two numeric values, specifying the lower limit and the upper limit of the y-axe scale. (optional) ## Returns The Manhattan plot. ## Examples ```r require(dplyr) # Import the data data("metaData") # Compute the inter-environment correlation matrix matCorr <- metaGE.cor(metaData, Threshold = 0.8) # Fit the Fixed Effect model FeDF <- metaGE.fit(metaData, matCorr, Method = "Fe") # Control the FDR (here Benjamini-Hochberg) Alpha <- 0.05 Signif <- FeDF$PVALUE %>% p.adjust(method = "BH") %>% `<`(Alpha) %>% which # Draw the corresponding manhattan plot PvalThresholdFe <- FeDF[Signif,]$PVALUE%>% max %>% max(.,0) manhattan_pval <- metaGE.manhattan(Data = FeDF,VarName = 'PVALUE', Threshold = PvalThresholdFe, Main = '-log10(Pval) alongside the chromosome Fe method') # Compute the score local xi <- 2 FeScore <- metaGE.lscore(FeDF,"PVALUE", xi) # Draw the corresponding manhattan plot manhattan_lscore <- metaGE.manhattan(Data = FeScore$Data,VarName = 'SCORE', SigZones = FeScore$SigZones, Score = TRUE, Main = 'Local score alongside the chromosome Fe method') ```

metaGE.manhattan function