## ----设置，包括= false ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ knitr::opts_chunk$set( collapse = TRUE, comment = "#>", crop = NULL ## Related to https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016656.html）## ----------- scp_framework，结果='markup'，fig.cap =“ s scp`依赖于singlecellexperiment”和“ qfeatures”和“ qfeatures”对象。out.width ='100％'，fig.align ='center'----- knitr :: include_graphics（“ ./ figures/scp_framework.png”，error = false）##）## ----消息= false--------------------------------------------------------------------------------------------库（SCP）数据（“ MQSCPDATA”）DIM（MQSCPDATA）## --------------------------------------------------------------------------------------------------------------------------------------（Quantcols<-grep（“ reporter.strententy。\\ d”，colnames（mqscpdata），value = true））## -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------头（MQSCPDATA [，QUANTCOLS]）## ---------------------------------------------------------------------------------------------------------------------------- head(mqScpData[, c("Charge"，“得分”，“ pep”，序列ce“，“长度”，“ retention.time”，“蛋白质”））## ------------------------------------------------------------------------------------- - - - - - - - - - - - - - - - - - - - - - - - 独特的（mqscpdata $ raw.file）## ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------数据（“ SampleanNotation”）头（SampleanNotation）## ------ fig.cap = "Linking the sample data to the feature data", echo = FALSE---- knitr::include_graphics("figures/readSCP_relation.png") ## ----readSCP------------------------------------------------------------------ scp <- readSCP(featureData = mqScpData, colData = sampleAnnotation, batchCol = "Raw.file", channelCol = "Channel", suffix = paste0("_TMT", 1:16), removeEmptyCols = TRUE) ## ----overview----------------------------------------------------------------- scp ## ----colData------------------------------------------------------------------ head(colData(scp)) ## ----rowData------------------------------------------------------------------ head(rowData(scp[["190222S_LCA9_X_FP94BM"]]))[, 1:5] ## ----assay-------------------------------------------------------------------- head(assay(scp, "190222S_LCA9_X_FP94BM")) ## ----setup2, include = FALSE-------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "", crop = NULL ) ## ----sessioninfo, echo=FALSE-------------------------------------------------- sessionInfo()