DataPreparation_EpitopeDataset: Compile epitope datasets retrieved from IEDB and other...

DataPreparation_EpitopeDatasetR Documentation

Compile epitope datasets retrieved from IEDB and other sources.

Description

Epitope_Import imports IEDB and other epitope files. Contradicting annotations on immunogenicity are internally resolved.
compressedToLongFormat converts a dataframe with a compresed column in which items are concatenated with "|" into a long-format one.
compressedToDummyDF generates dummy variable columns from a compresed column in which items are concatenated with "|".

Usage

Epitope_Import(
  IEDBAssayFileName = NULL,
  OtherFileNames = NULL,
  peptideLengthSet = 8:11
)

compressedToLongFormat(df, compressedColumnName)

compressedToDummyDF(df, compressedColumnName)

Arguments

IEDBAssayFileName

A set of T cell assay results obtained from IEDB.

OtherFileNames

Other epitope source files. Must contain a "Dataset" column indicating the data source.

peptideLengthSet

A set of peptide lengths to be incorporated.

df

A dataframe/datatable of epitope dataset.

compressedColumnName

A string indicating the names of the compressed column to be converted into a long format.


masato-ogishi/Repitope documentation built on Feb. 14, 2023, 5:47 a.m.