mycobacrvR (version 1.1)

iedb_consensus_mhci_nmer: Epitope conservation prediction for MHCI using IEDB-consensus information

Description

iedb_consensus_mhci_nmer is a method to predict conservation of epitopes among orthologs for MHCI using IEDB-consensus server data

Usage

iedb_consensus_mhci_nmer(epi_length)

Arguments

epi_length

A character vector of epitope length

Value

iedb_consensus_mhci_nmer() will write two files in the working directory. One file contains the information of epitope and the other file contains metadata for epitope showing orthologs of H37Rv

Details

This function takes epitope length as input into epi_length object. Input data for this function is present in "/data_mycobacrvR/IEDBconsensus_mhci_out" directory, therefore set working directory to "~/data_mycobacrvR/IEDBconsensus_mhci_out/" before using this function. IEDB server provides epitopes by selecting window size of epitope length such as 8, 9, 10. Therefore epi_length should be given as "10mer".

Examples

# NOT RUN {
iedb_consensus_mhci_nmer("IEDB_consensus_mhci")
# }
# NOT RUN {
##Conservation of epitopes from IEDB server
# }