Nothing
## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----style, echo=FALSE, results='asis'----------------------------------------
BiocStyle::markdown()
## ----setup, echo=FALSE, message=FALSE-----------------------------------------
library(MSstatsPTM)
## ----install, eval=FALSE------------------------------------------------------
# devtools::install_github("tsunghengtsai/MSstatsPTM")
## ----lib, eval=FALSE----------------------------------------------------------
# library(MSstatsPTM)
## ----simulate-----------------------------------------------------------------
# sim <- PTMsimulateExperiment(
# nGroup=2, nRep=2, nProtein=1, nSite=2, nFeature=5,
# mu=list(PTM=25, PROTEIN=25),
# delta=list(PTM=c(0, 1), PROTEIN=c(0, 1)),
# sRep=list(PTM=0.2, PROTEIN=0.2),
# sPeak=list(PTM=0.05, PROTEIN=0.05)
# )
sim <- PTMsimulateExperiment(
nGroup=2, nRep=2, nProtein=1, nSite=2, nFeature=5,
logAbundance=list(
PTM=list(mu=25, delta=c(0, 1), sRep=0.2, sPeak=0.05),
PROTEIN=list(mu=25, delta=c(0, 1), sRep=0.2, sPeak=0.05)
)
)
## ----data-structure-----------------------------------------------------------
str(sim)
## ----data-ptm-----------------------------------------------------------------
sim[["PTM"]]
## ----data-protein-------------------------------------------------------------
sim[["PROTEIN"]]
## ----fasta, eval=FALSE--------------------------------------------------------
# fas <- tidyFasta("https://www.uniprot.org/uniprot/P37840.fasta")
## ----normalization, message=FALSE---------------------------------------------
normalized <- PTMnormalize(sim, method="median")
normalized
## ----normalization-ref, message=FALSE-----------------------------------------
refs <- list(
PTM=data.frame(run=paste0("R_", 1:4), adjLog2inty=c(2, -2, 0, 0)),
PROTEIN=data.frame(run=paste0("R_", 1:4), adjLog2inty=c(3, -1, 0, 0))
)
PTMnormalize(sim, method="ref", refs=refs)
## ----summarization, message=FALSE---------------------------------------------
summarized <- PTMsummarize(normalized)
summarized
## ----estimation, message=FALSE------------------------------------------------
estimates <- PTMestimate(summarized)
estimates
## -----------------------------------------------------------------------------
PTMcompareMeans(estimates, controls="G_1", cases="G_2")
## -----------------------------------------------------------------------------
PTMcompareMeans(estimates, controls="G_1", cases="G_2", adjProtein=TRUE)
## ----session------------------------------------------------------------------
sessionInfo()
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