peptideLibraries {PhIPData}R Documentation

Peptide libraries

Description

PhIP-Seq experiments often use identical peptide libraries different cohorts. These functions enable the user to conveniently reuse tidied libraries.

Usage

getLibraryPath()

setLibraryPath(path)

getLibrary(name)

makeLibrary(library, name)

Arguments

path

path to a folder containing a .rds files for each library

name

name of the library

library

a matrix, data.frame, or DataFrame with the peptide information for the specified library.

Details

Each library is stored as a DataFrame in .rds file. By default the libraries are stored in the libraries package folder. setLibraryPath allows the user to change the location of this library, if desired.

While libraries can be directly saved in the specified format by the user, it is highly recommended to use the makeLibrary function to save a new library.

Value

getLibraryPath returns the path to the directory containing .rds files for each library. getLibrary returns a DataFrame corresponding to the peptide information for the specified library.

Functions

Examples

## Get and set path to libraries folder
getLibraryPath()
## Not run: setLibraryPath("examplepath/")

## Create a new library
pep_meta <- data.frame(species = c(rep("human immunodeficiency virus", 3),
     rep("Epstein-Barr virus", 2)))
makeLibrary(pep_meta, "new_library")

## Use new library
counts_dat <- matrix(1:10, nrow = 5)
phip_obj <- PhIPData(counts = counts_dat,
     peptideInfo = getLibrary("new_library"))

## Delete created library
file.remove(paste0(getLibraryPath(), "/new_library.rds"))


[Package PhIPData version 1.0.0 Index]