## ---- include=FALSE, echo=FALSE----------------------------------------------- # date: "`r doc_date()`" # "`r pkg_ver('BiocStyle')`" # ## ---- echo=FALSE-------------------------------------------------------------- library(MSPrep) ## ----------------------------------------------------------------------------- data(msquant) colnames(msquant)[3] ## ----------------------------------------------------------------------------- summarizedDF <- msSummarize(msquant, cvMax = 0.50, minPropPresent = 1/3, compVars = c("mz", "rt"), sampleVars = c("spike", "batch", "replicate", "subject_id"), colExtraText = "Neutral_Operator_Dif_Pos_", separator = "_", missingValue = 1) ## ---- echo = FALSE------------------------------------------------------------ summarizedDF[1:10, 1:6] ## ----------------------------------------------------------------------------- filteredDF <- msFilter(summarizedDF, filterPercent = 0.8, compVars = c("mz", "rt"), sampleVars = c("spike", "batch", "subject_id"), separator = "_") ## ---- echo = FALSE------------------------------------------------------------ filteredDF[1:10, 1:6] ## ----------------------------------------------------------------------------- imputedDF <- msImpute(filteredDF, imputeMethod = "knn", compVars = c("mz", "rt"), sampleVars = c("spike", "batch", "subject_id"), separator = "_", returnToSE = FALSE, missingValue = 0) ## ---- echo = FALSE------------------------------------------------------------ imputedDF[1:10, 1:6] ## ---- message = FALSE, results = 'hide'--------------------------------------- normalizedDF <- msNormalize(imputedDF, normalizeMethod = "quantile + ComBat", transform = "log10", compVars = c("mz", "rt"), sampleVars = c("spike", "batch", "subject_id"), covariatesOfInterest = c("spike"), separator = "_") ## ---- echo = FALSE------------------------------------------------------------ normalizedDF[1:10, 1:6] ## ---- message = FALSE, results = 'hide'--------------------------------------- preparedDF <- msPrepare(msquant, minPropPresent = 1/3, missingValue = 1, filterPercent = 0.8, imputeMethod = "knn", normalizeMethod = "quantile + ComBat", transform = "log10", covariatesOfInterest = c("spike"), compVars = c("mz", "rt"), sampleVars = c("spike", "batch", "replicate", "subject_id"), colExtraText = "Neutral_Operator_Dif_Pos_", separator = "_") ## ---- echo = FALSE------------------------------------------------------------ preparedDF[1:10, 1:6] ## ----------------------------------------------------------------------------- data(COPD_131) summarizedSE131 <- msSummarize(COPD_131, cvMax = 0.5, minPropPresent = 1/3, replicate = "replicate", compVars = c("Mass", "Retention.Time", "Compound.Name"), sampleVars = c("subject_id", "replicate"), colExtraText = "X", separator = "_", returnToSE = TRUE) ## ---- echo = FALSE------------------------------------------------------------ #head(assay(summarizedSE131)) ## ----------------------------------------------------------------------------- filteredSE131 <- msFilter(summarizedSE131, filterPercent = 0.8) ## ---- echo = FALSE------------------------------------------------------------ #head(assay(filteredSE131)) ## ----------------------------------------------------------------------------- imputedSE131 <- msImpute(filteredSE131, imputeMethod = "bpca", nPcs = 3, missingValue = 0) ## ----------------------------------------------------------------------------- normalizedSe131 <- msNormalize(imputedSE131, normalizeMethod = "median", transform = "none") ## ---- echo = FALSE------------------------------------------------------------ #head(assay(imputedSE131)) ## ----------------------------------------------------------------------------- preparedSE <- msPrepare(COPD_131, cvMax = 0.5, minPropPresent = 1/3, compVars = c("Mass", "Retention.Time", "Compound.Name"), sampleVars = c("subject_id", "replicate"), colExtraText = "X", separator = "_", filterPercent = 0.8, imputeMethod = "bpca", normalizeMethod = "median", transform = "none", nPcs = 3, missingValue = 0, returnToSE = TRUE) ## ---- echo = FALSE------------------------------------------------------------ #head(assay(imputedSE131)) ## ----------------------------------------------------------------------------- sessionInfo()