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DepLabData

Data from Noah Dephoure's lab at Weill Cornell Medical College

Installation

To install the latest version directly from Github, please use:

install.packages("devtools")
devtools::install_github("julia-wrobel/DepLabData")

Help file

To see what datasets are available in the package, please use:


library(help = "DepLabData")

Go from wide to long format

For this functionality, please install the DepLab package:

devtools::install_github("NCBI-Hackathons/Proteomic_Correlation_Shiny", subdir = "DepLab")

To convert from wide to long format:

library(DepLab)
# load the data in wide format --> every row corresponds to one protein, but the columns contain
# values for at least 7 variables (x 30 fractions)
data(WT_trial1)

# extract protein IDs
ids <- extract_proteinID(WT_trial1$Protein.IDs, routine = "human")

# extract only values from "raw.intensity" columns
# and return a long data.frame
WT1_raw.intensity <- MQ_to_longFormat(WT_trial1, y= "raw.intensity", return.dt = TRUE, ids)

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