Nothing
## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.width=6,
fig.height=6
)
## ---- message=FALSE, warning=FALSE--------------------------------------------
library(MSstatsTMTPTM)
library(MSstatsTMT)
## ---- eval = FALSE------------------------------------------------------------
# if (!requireNamespace("BiocManager", quietly = TRUE))
# install.packages("BiocManager")
#
# BiocManager::install("MSstatsTMTPTM")
## -----------------------------------------------------------------------------
# read in raw data files
# raw.ptm <- read.csv(file="raw.ptm.csv", header=TRUE)
# raw.protein <- read.csv(file="raw.protein.csv", header=TRUE)
head(raw.ptm)
head(raw.protein)
## ---- results='hide', message=FALSE, warning=FALSE----------------------------
# Run MSstatsTMT proteinSummarization function
quant.msstats.ptm <- proteinSummarization(raw.ptm,
method = "msstats",
global_norm = TRUE,
reference_norm = FALSE,
MBimpute = TRUE)
quant.msstats.protein <- proteinSummarization(raw.protein,
method = "msstats",
global_norm = TRUE,
reference_norm = FALSE,
MBimpute = TRUE)
## -----------------------------------------------------------------------------
head(quant.msstats.ptm)
head(quant.msstats.protein)
# Profile Plot
dataProcessPlotsTMTPTM(data.ptm=raw.ptm,
data.protein=raw.protein,
data.ptm.summarization=quant.msstats.ptm,
data.protein.summarization=quant.msstats.protein,
type='ProfilePlot'
)
# Quality Control Plot
# dataProcessPlotsTMTPTM(data.ptm=ptm.input.pd,
# data.protein=protein.input.pd,
# data.ptm.summarization=quant.msstats.ptm,
# data.protein.summarization=quant.msstats.protein,
# type='QCPlot')
## ----message = FALSE, warning = FALSE-----------------------------------------
# test for all the possible pairs of conditions
model.results.pairwise <- groupComparisonTMTPTM(data.ptm=quant.msstats.ptm,
data.protein=quant.msstats.protein)
names(model.results.pairwise)
head(model.results.pairwise[[1]])
# Load specific contrast matrix
#example.contrast.matrix <- read.csv(file="example.contrast.matrix.csv", header=TRUE)
example.contrast.matrix
# test for specified condition comparisons only
model.results.contrast <- groupComparisonTMTPTM(data.ptm=quant.msstats.ptm,
data.protein=quant.msstats.protein,
contrast.matrix = example.contrast.matrix)
names(model.results.contrast)
head(model.results.contrast[[1]])
## ----session------------------------------------------------------------------
sessionInfo()
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