peptideLibraries: Peptide libraries

In athchen/PhIPData: Container for PhIP-Seq Experiments

Description

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

Usage

getLibrary(name)

makeLibrary(library, name)

removeLibrary(name)

listLibrary()

Arguments

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. New libraries can be stored for future use with the makeLibrary function.

Value

getLibrary returns a DataFrame corresponding to the peptide information for the specified library.

Functions

• getLibrary: return a DataFrame with the peptide information corresponding to the library.

• makeLibrary: create and store a DataFrame with the specified peptide information.

• removeLibrary: delete stored libraries

• listLibrary: list all available libraries

Examples

## 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")
)

## List libraries
listLibrary()

## Delete created library
removeLibrary("new_library")

athchen/PhIPData documentation built on Feb. 10, 2022, 1:34 a.m.