## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", crop = NULL ## cf to https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016656.html ) ## ----fig.cap="The `scp` framework relies on `SingleCellExperiment` and `QFeatures` objects", echo=FALSE, out.width='100%', fig.align='center'---- knitr::include_graphics("./figures/SCP_framework.png") ## ----message = FALSE---------------------------------------------------------- library(scp) data("mqScpData") dim(mqScpData) ## ----echo=FALSE, out.width='60%', fig.cap="Conceptual representation of the input table", fig.align = 'center'---- knitr::include_graphics('figures/readSCP_inputTable.png') ## ----------------------------------------------------------------------------- (quantCols <- grep("Reporter.intensity.\\d", colnames(mqScpData), value = TRUE)) ## ----------------------------------------------------------------------------- head(mqScpData[, quantCols]) ## ----------------------------------------------------------------------------- head(mqScpData[, c("Charge", "Score", "PEP", "Sequence", "Length", "Retention.time", "Proteins")]) ## ----------------------------------------------------------------------------- unique(mqScpData$Raw.file) ## ----------------------------------------------------------------------------- data("sampleAnnotation") head(sampleAnnotation) ## ----echo=FALSE, out.width='60%', fig.cap="Conceptual representation of the sample table", fig.align = 'center'---- knitr::include_graphics('figures/readSCP_sampleTable.png') ## ----readSCP------------------------------------------------------------------ scp <- readSCP(featureData = mqScpData, colData = sampleAnnotation, batchCol = "Raw.file", channelCol = "Channel", suffix = paste0("_TMT", 1:16), removeEmptyCols = TRUE) scp ## ----colData------------------------------------------------------------------ head(colData(scp)) ## ----rowData------------------------------------------------------------------ head(rowData(scp[["190222S_LCA9_X_FP94BM"]]))[, 1:5] ## ----assay-------------------------------------------------------------------- head(assay(scp, "190222S_LCA9_X_FP94BM")) ## ----echo=FALSE, out.width='60%', fig.cap="Step1: Convert the input table to a `SingleCellExperiment` object", fig.align = 'center'---- knitr::include_graphics('figures/readSCP_step1.png') ## ----echo=FALSE, out.width='65%', fig.cap="Step2: Split by acquisition run", fig.align = 'center'---- knitr::include_graphics('figures/readSCP_step2.png') ## ----echo=FALSE, out.width='100%', fig.cap="Step3: Adding and matching the sample annotations", fig.align = 'center'---- knitr::include_graphics('figures/readSCP_step3.png') ## ----echo=FALSE, out.width='80%', fig.cap="Step4: Convert to a `QFeatures`", fig.align = 'center'---- knitr::include_graphics('figures/readSCP_step4.png') ## ----setup2, include = FALSE-------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "", crop = NULL ) ## ----sessioninfo, echo=FALSE-------------------------------------------------- sessionInfo()