## ----style, echo = FALSE, results = 'asis'------------------------------------ BiocStyle::markdown() ## ---- echo = FALSE, warning = FALSE, message = FALSE-------------------------- library(MsFeatures) library(SummarizedExperiment) ## ----load-data, message = FALSE----------------------------------------------- library(MsFeatures) library(SummarizedExperiment) data("se") ## ----fdev--------------------------------------------------------------------- rowData(se) head(assay(se)) ## ----feature-rt-mz-plot, fig.width = 8, fig.height = 6, fig.cap = "Plot of retention times and m/z for all features in the data set."---- plot(rowData(se)$rtmed, rowData(se)$mzmed, xlab = "retention time", ylab = "m/z", main = "features", col = "#00000060") grid() ## ----------------------------------------------------------------------------- se <- groupFeatures(se, param = SimilarRtimeParam(10), rtime = "rtmed") ## ----------------------------------------------------------------------------- table(featureGroups(se)) ## ----------------------------------------------------------------------------- split(rowData(se)$rtmed, featureGroups(se)) |> vapply(FUN = mean, numeric(1)) |> sort() ## ----abundance-correlation-heatmap, fig.cap = "Correlation of features based on their abundances.", fig.width = 12, fig.height = 14---- library(pheatmap) fvals <- log2(assay(se)) cormat <- cor(t(fvals), use = "pairwise.complete.obs") ann <- data.frame(fgroup = featureGroups(se)) rownames(ann) <- rownames(cormat) res <- pheatmap(cormat, annotation_row = ann, cluster_rows = TRUE, cluster_cols = TRUE) ## ----abundance-correlation---------------------------------------------------- se <- groupFeatures(se, AbundanceSimilarityParam(threshold = 0.7, transform = log2), i = 1) table(featureGroups(se)) ## ----abundance-correlation-fg003, fig.width = 8, fig.height = 8, fig.cap = "Pairwise correlation plot for features initially grouped into the feature group FG.003."---- fts <- grep("FG.003", featureGroups(se)) pairs(t(fvals[fts, ]), gap = 0.1, main = "FG.003") ## ----abundance-correlation-fg008, fig.width = 8, fig.height = 8, fig.cap = "Pairwise correlation plot for features initially grouped into the feature group FG.008."---- fts <- grep("FG.008", featureGroups(se)) pairs(t(fvals[fts, ]), gap = 0.1, main = "FG.008") ## ----abundance-correlation-fg008-table, results = "asis"---------------------- tmp <- as.data.frame(rowData(se)[fts, c("rtmed", "mzmed", "feature_group")]) tmp <- tmp[order(tmp$feature_group), ] knitr::kable(tmp) ## ----------------------------------------------------------------------------- featureGroups(se) <- NA_character_ featureGroups(se)[30:60] <- "FG" se <- groupFeatures(se, SimilarRtimeParam(10), rtime = "rtmed") ## ----------------------------------------------------------------------------- featureGroups(se) ## ----sessioninfo, echo=FALSE-------------------------------------------------- sessionInfo()