In barzine/barzinePhdData: Data to be used with barzinePhdR

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(barzinePhdData)
library(barzinePhdR)

Proteomics

Pandey

Top3

pandey.origin<-barzinePhdR::Read.table(filename =
                                         system.file("extdata",'pandey_expression_filtered.txt',
                                                        package = "barzinePhdData"),
                                       na.strings='-',
                                       comment.char = "@")

pandey.origin_noCluster<-removeClusters(pandey.origin,
                                        path=system.file("extdata", 
                                                         "pandey_expression_table.txt",
                                                         package = "barzinePhdData"))

pandey.nc<-extractWithinSampleAbundance(pandey.origin_noCluster)
pandey.nc<-NAto0(pandey.nc)

pandey.top3<-fixNamesPandey(pandey.nc,method="top3")

pandey.top3<-barzinePhdR::strip(pandey.top3)

colPandey<-c("Adrenal", "Colon", "Oesophagus", "Gallbladder", "Heart",
             "Kidney", "Liver", "Lung", "Ovary", "Pancreas", "Placenta", "Prostate",
             "Rectum", "Testis", "Urinarybladder")

pandey.top3.15<-barzinePhdR::strip(pandey.top3[,colPandey])

PPKM

pandey.ppkm<-barzinePhdR::Read.table(filename =
                          system.file("extdata",'EnsembleGenePPKM_V3_Pandey.txt',
                                                        package = "barzinePhdData"),
                        na.strings='x')
pandey.ppkm<-NAto0(pandey.ppkm)
pandey.ppkm<-fixNamesPandey(pandey.ppkm,'ppkm')
pandey.ppkm<-barzinePhdR::strip(pandey.ppkm)

pandey.ppkm.15<-barzinePhdR::strip(pandey.ppkm[,colPandey])

PPM

pandey.ppm<-barzinePhdR::Read.table(filename =
                          system.file("extdata","EnsembleGenePPM_V3_Pandey.txt",
                                      package = "barzinePhdData"),
                       na.strings='x')
pandey.ppm<-NAto0(pandey.ppm)
pandey.ppm<-fixNamesPandey(pandey.ppm,method='ppm')
pandey.ppm<-barzinePhdR::strip(pandey.ppm)

pandey.ppm.15<-barzinePhdR::strip(pandey.ppm[,colPandey])

Kuster

Top3

kuster.origin<-barzinePhdR::Read.table(filename =
                                         system.file("extdata",'kuster_expression_filtered.txt',
                                                        package = "barzinePhdData"),
                                       na.strings='-',
                                       comment.char = "@")

kuster.origin_noCluster<-removeClusters(kuster.origin,
                                        path=system.file("extdata", 
                                                         "kuster_expression_table.txt",
                                                         package = "barzinePhdData"))

kuster.nc<-extractWithinSampleTop3Abundance(kuster.origin_noCluster)
kuster.nc<-NAto0(kuster.nc)

kuster.top3.all<-fixNamesKuster(kuster.nc)
kuster.top3.all<-barzinePhdR::strip(kuster.top3.all)

kuster.top3<-mergeUterus(kuster.top3.all)
kuster.top3<-barzinePhdR::strip(kuster.top3)

PPKM

kuster.ppkm.all<-barzinePhdR::Read.table(filename =
                          system.file("extdata",'EnsembleGenePPKM_V3_Kuster.txt',
                                                        package = "barzinePhdData"),
                        na.strings='x')
kuster.ppkm.all<-NAto0(kuster.ppkm.all)
kuster.ppkm.all<-fixNamesKuster(kuster.ppkm.all)
kuster.ppkm.all<-barzinePhdR::strip(kuster.ppkm.all)

kuster.ppkm<-barzinePhdR::strip(mergeUterus(kuster.ppkm.all))

PPM

kuster.ppm.all<-barzinePhdR::Read.table(filename =
                          system.file("extdata","EnsembleGenePPM_V3_Kuster.txt",
                                      package = "barzinePhdData"),
                       na.strings='x')
kuster.ppm.all<-NAto0(kuster.ppm.all)
kuster.ppm.all<-fixNamesKuster(kuster.ppm.all)
kuster.ppm.all<-barzinePhdR::strip(kuster.ppm.all)

kuster.ppm<-barzinePhdR::strip(mergeUterus(kuster.ppm.all))

Cutler

cutler.origin<-barzinePhdR::Read.table(filename =
                                         system.file("extdata",'cutler_expression_filtered.txt',
                                                        package = "barzinePhdData"),
                                       na.strings='-',
                                       comment.char = "@")

cutler.origin_noCluster<-removeClusters(cutler.origin,
                                        path=system.file("extdata", 
                                                         "cutler_expression_table.txt",
                                                         package = "barzinePhdData"))

cutler.nc<-extractWithinSampleTop3Abundance(cutler.origin_noCluster)
cutler.nc<-NAto0(cutler.nc)

cutler.top3<-fixNamesCutler(cutler.nc)

cutler.top3<-barzinePhdR::strip(cutler.top3)