Nothing
## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.width=8,
fig.height=8
)
## ---- message=FALSE, warning=FALSE--------------------------------------------
library(MSstatsTMTPTM)
library(MSstatsTMT)
library(MSstats)
library(dplyr)
## ---- 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)
head(raw.ptm)
## -----------------------------------------------------------------------------
head(raw.protein)
# raw.protein <- read.csv(file="raw.protein.csv", header=TRUE)
## ---- results='hide', message=FALSE, warning=FALSE----------------------------
# Use proteinSummarization function from MSstatsTMT to summarize raw data
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)
## ---- results='hide', 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)
## ---- message=FALSE, warning=FALSE-------------------------------------------
# Specify comparisons
comparison<-matrix(c(1,0,0,-1,0,0,
0,1,0,0,-1,0,
0,0,-1,0,0,-1,
1,0,-1,0,0,0,
0,1,-1,0,0,0,
0,0,0,1,0,-1,
0,0,0,0,1,-1,
.25,.25,-.5,.25,.25,-.5,
1/3,1/3,1/3,-1/3,-1/3,-1/3),nrow=9, ncol=6, byrow=TRUE)
# Set the names of each row
row.names(comparison)<-c('1-4', '2-5', '3-6', '1-3',
'2-3', '4-6', '5-6', 'Partial', 'Third')
# Set the column names
colnames(comparison)<- c('Condition_1', 'Condition_2', 'Condition_3',
'Condition_4', 'Condition_5', 'Condition_6')
comparison
## ---- results='hide', message=FALSE, warning=FALSE----------------------------
# test for specified condition comparisons only
model.results.contrast <- groupComparisonTMTPTM(data.ptm=quant.msstats.ptm,
data.protein=quant.msstats.protein,
contrast.matrix = comparison)
## -----------------------------------------------------------------------------
names(model.results.contrast)
ptm_model <- model.results.contrast[[1]]
protein_model <- model.results.contrast[[2]]
adjusted_model <- model.results.contrast[[3]]
head(adjusted_model)
## -----------------------------------------------------------------------------
groupComparisonPlots(data = adjusted_model,
type = 'VolcanoPlot',
ProteinName = FALSE,
which.Comparison = '1-4',
address = FALSE)
## -----------------------------------------------------------------------------
dataProcessPlotsTMTPTM(data.ptm = raw.ptm,
data.protein = raw.protein,
data.ptm.summarization = quant.msstats.ptm,
data.protein.summarization = quant.msstats.protein,
type = 'ProfilePlot',
which.Protein = 'Protein_2391_Y40',
address = FALSE)
## -----------------------------------------------------------------------------
dataProcessPlotsTMTPTM(data.ptm = raw.ptm %>% filter(
Condition %in% c('Condition_1', 'Condition_4')),
data.protein = raw.protein %>% filter(
Condition %in% c('Condition_1', 'Condition_4')),
data.ptm.summarization = quant.msstats.ptm %>% filter(
Condition %in% c('Condition_1', 'Condition_4')),
data.protein.summarization =
quant.msstats.protein %>% filter(Condition %in% c(
'Condition_1', 'Condition_4')),
type = 'ProfilePlot',
which.Protein = 'Protein_2391_Y40',
originalPlot = FALSE,
address = FALSE)
model_df <- rbind(adjusted_model %>% filter(
Protein == 'Protein_2391_Y40' & Label == '1-4') %>% select(-Tvalue),
ptm_model %>% filter(
Protein == 'Protein_2391_Y40' & Label == '1-4'
) %>% select(-issue),
protein_model %>% filter(
Protein == 'Protein_2391' & Label == '1-4'
) %>% select(-issue))
model_df <- data.frame(model_df)
rownames(model_df) <- c('Adjusted PTM', 'PTM', 'Protein')
model_df
## -----------------------------------------------------------------------------
dataProcessPlotsTMTPTM(data.ptm = raw.ptm %>% filter(
Condition %in% c('Condition_2', 'Condition_5')),
data.protein = raw.protein %>% filter(
Condition %in% c('Condition_2', 'Condition_5')),
data.ptm.summarization = quant.msstats.ptm %>%
filter(Condition %in% c('Condition_2', 'Condition_5')),
data.protein.summarization = quant.msstats.protein %>%
filter(Condition %in% c('Condition_2', 'Condition_5')),
type = 'ProfilePlot',
which.Protein = 'Protein_1076_Y67',
originalPlot = FALSE,
address = FALSE)
model_df <- rbind(adjusted_model %>% filter(
Protein == 'Protein_1076_Y67' & Label == '2-5') %>% select(-Tvalue),
ptm_model %>% filter(
Protein == 'Protein_1076_Y67' & Label == '2-5'
) %>% select(-issue),
protein_model %>% filter(
Protein == 'Protein_1076' & Label == '2-5'
) %>% select(-issue))
model_df <- data.frame(model_df)
rownames(model_df) <- c('Adjusted PTM', 'PTM', 'Protein')
model_df
## ----session------------------------------------------------------------------
sessionInfo()
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