| Title: | Integrative Immunoinformatics for Mycobacterial Diseases in R Platform |
|---|---|
| Description: | The mycobacrvR package contains utilities to provide detailed information for B cell and T cell epitopes for predicted adhesins from various servers such as ABCpred, Bcepred, Bimas, Propred, NetMHC and IEDB. Please refer the URL below to download data files (data_mycobacrvR.zip) used in functions of this package. |
| Authors: | Deepika Kulshreshtha, Rupanjali Chaudhuri, Surabhi Seth, S. Ramachandran |
| Maintainer: | S. Ramachandran<[email protected]> |
| License: | GPL-2 |
| Version: | 1.1 |
| Built: | 2024-12-06 06:38:17 UTC |
| Source: | CRAN |
abcpred_nmer is a method to predict conservation of epitopes among orthologs from ABCPred server data
abcpred_nmer(epi_length)abcpred_nmer(epi_length)
epi_length |
A character vector of epitope length |
This function takes epitope length as input into epi_length object. Input data for this function is present in "/data_mycobacrvR/abcpred_out" directory, therefore set this directory as working directory before using this function. ABCPred server provide epitopes by selecting window size of epitope length such as 10, 12, 14, 16, 18, 20. Therefore epi_length should be given as "10mer".
abcpred_nmer() will write two files in the working directory. One file contains the information of epitope and the other file contains metadata for epitope that shows orthologs of H37Rv contating that epitope
Deepika Kulshreshtha
## Not run: abcpred_nmer("10mer") ##Conservation of all 10mer epitopes from ABCPred server## Not run: abcpred_nmer("10mer") ##Conservation of all 10mer epitopes from ABCPred server
algpred is a function to filter allergic and non allergic proteins of an organism using output of Algpred
algpred(data, organism, ginumber, prediction)algpred(data, organism, ginumber, prediction)
data |
A character string specifying filenamme containing tabular output from Algpred |
organism |
A character vector specifying name of species present in "organism.txt" |
ginumber |
A numeric vector specifying ginumber of protein for a species for which allergic preperty is to be predicted |
prediction |
A character vector specifying "Allergen" or "Non Allergen" |
This function takes tabular output of Algpred in data as input.Input data (Final_algpred.txt) for this function is present in "/data_mycobacrvR/" directory, therefore set working directory to "~/data_mycobacrvR/" before using this function. algpred() filters data using arguments organism, ginumber and prediction. Defalult value for ginumber is "ALL" and for prediction is "Non Allergen". Organism can be provided by selecting organisms from "organism.txt" file present in working directory
A file of filtered proteins named "filtered_algpred.txt" using the given arguments.
Deepika Kulshreshtha
## Not run: algpred("Final_algpred.txt",organism="Mycobacterium avium 104")## Not run: algpred("Final_algpred.txt",organism="Mycobacterium avium 104")
allermatch is a function to filter allergic and non allergic proteins of an organism using output of Allermatch
allermatch(data, organism, ginumber, prediction)allermatch(data, organism, ginumber, prediction)
data |
A character string specifying filenamme containing tabular output from Allermatch |
organism |
A character vector specifying name of species present in organism.txt |
ginumber |
A numeric vector specifying ginumber of protein for a species for which allergic preperty is to be predicted |
prediction |
A character vector specifying "Allergen" or "Non Allergen" |
This function takes tabular output of Allermatch in data as input.Input data (Final_allermatch.txt) for this function is present in "/data_mycobacrvR/" directory, therefore set working directory to "~/data_mycobacrvR/" before using this function. allermatch() filters data using arguments organism, ginumber and prediction. Defalult value for ginumber is "ALL" and for prediction is "Non Allergen". Organism can be provided by selecting organisms from "organism.txt" file present in working directory
A file of filtered proteins named "filtered_allermatch.txt" using the given arguments.
Deepika Kulshreshtha
## Not run: allermatch("Final_allermatch.txt",organism="Mycobacterium avium 104")## Not run: allermatch("Final_allermatch.txt",organism="Mycobacterium avium 104")
bcepred_nmer is a method to predict conservation of epitopes among orthologs from Bcepred server data
bcepred_nmer(clas)bcepred_nmer(clas)
clas |
A character vector for server name |
This function takes server name "bcepred" as input into clas object. Input data for this function is present in "/data_mycobacrvR/bcepred_out" directory, therefore set working directory to "~/data_mycobacrvR/bcepred_out/" before using this function. Bcepred server provides epitopes of different length.
bcepred_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
Deepika Kulshreshtha
## Not run: bcepred_nmer("bcepred")##Conservation of epitopes from Bcepred server## Not run: bcepred_nmer("bcepred")##Conservation of epitopes from Bcepred server
bimas_nmer is a method to predict conservation of epitopes among orthologs from Bimas server data
bimas_nmer(epi_length)bimas_nmer(epi_length)
epi_length |
A character vector of epitope length |
This function takes epitope length as input into epi_length object. Input data for this function is present in "/data_mycobacrvR/bimas_out" directory, therefore set this directory as working directory before using this function. Bimas server provide epitopes by selecting window size of epitope length such as 8, 9 and 10. Therefore epi_length should be given as "10mer".
bimas_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
Deepika Kulshreshtha
## Not run: bimas_nmer("10mer") ##Conservation of 10mer epitopes from Bimas server## Not run: bimas_nmer("10mer") ##Conservation of 10mer epitopes from Bimas server
filter.firstlayer is a function to filter first layer data
filter.firstlayer(data, organism, ginumber, spaanscore, subcelllocal, tmhelices, Hrefhits)filter.firstlayer(data, organism, ginumber, spaanscore, subcelllocal, tmhelices, Hrefhits)
data |
A character string specifying filenamme containing first layer data table |
organism |
A character vector specifying species name present in "organism.txt" |
ginumber |
A numeric vector specifying ginumber |
spaanscore |
A numeric vector specifying SPAAN score threshold |
subcelllocal |
A character vector specifying location of the protein |
tmhelices |
A numeric vectr specifying number of TM helix |
Hrefhits |
A character vector specifying non similarity to Human Reference Proteins |
This function filters the first layer data according to "motif and topology", "subcellular location" and "homology". Input data (firstlayer.txt) for this function is present in "/data_mycobacrvR/" directory, therefore set working directory to "~/data_mycobacrvR/" before using this function. Defalult value for ginumber,spaanscore,subcelllocal,tmhelices and Hrefhits is "ALL", >0.6, "Extracellular OR Cellwall", <2 and "No Hits found"
A file of filtered proteins named "filtered_firstlayer.txt" using the given arguments
Deepika Kulshreshtha, Rupanjali Chaudhuri, S. Ramachandran
## Not run: filter.firstlayer("firstlayer.txt",organism="Mycobacterium avium 104")## Not run: filter.firstlayer("firstlayer.txt",organism="Mycobacterium avium 104")
iedb_arb_mhci_nmer is a method to predict conservation of epitopes among orthologs for MHCI using IEDB-ARB server data
iedb_arb_mhci_nmer(clas)iedb_arb_mhci_nmer(clas)
clas |
A character vector for server name |
This function takes server name "IEDB_arb_mhci" as input into clas object. Input data for this function is present in "/data_mycobacrvR/IEDBarb_mhci_out" directory, therefore set working directory to "~/data_mycobacrvR/IEDBarb_mhci_out/" before using this function. IEDB-ARB server provides epitopes of different length.
iedb_arb_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
Deepika Kulshreshtha
## Not run: iedb_arb_mhci_nmer("IEDB_arb_mhci") ##Conservation of all epitopes from IEDB server## Not run: iedb_arb_mhci_nmer("IEDB_arb_mhci") ##Conservation of all epitopes from IEDB server
iedb_arb_mhcii_nmer is a method to predict conservation of epitopes among orthologs for MHCII using IEDB-ARB server data
iedb_arb_mhcii_nmer(clas)iedb_arb_mhcii_nmer(clas)
clas |
A character vector for server name |
This function takes server name "IEDB_arbMHCII" as input into clas object. Input data for this function is present in "/data_mycobacrvR/iedb_arb_mhcii_out" directory, therefore set working directory to "~/data_mycobacrvR/iedb_arb_mhcii_out/" before using this function. IEDB-ARB server provides epitopes of different length.
iedb_arb_mhcii_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
Deepika Kulshreshtha
## Not run: iedb_arb_mhcii_nmer("IEDB_arb_mhcii") ##Conservation of all epitopes from IEDB server## Not run: iedb_arb_mhcii_nmer("IEDB_arb_mhcii") ##Conservation of all epitopes from IEDB server
iedb_consensus_mhci_nmer is a method to predict conservation of epitopes among orthologs for MHCI using IEDB-consensus server data
iedb_consensus_mhci_nmer(epi_length)iedb_consensus_mhci_nmer(epi_length)
epi_length |
A character vector of epitope length |
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".
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
Deepika Kulshreshtha
## Not run: iedb_consensus_mhci_nmer("IEDB_consensus_mhci") ##Conservation of epitopes from IEDB server## Not run: iedb_consensus_mhci_nmer("IEDB_consensus_mhci") ##Conservation of epitopes from IEDB server
iedb_consensus_mhcii_nmer is a method to predict conservation of epitopes among orthologs for MHCII using IEDB-consensus server data
iedb_consensus_mhcii_nmer(clas)iedb_consensus_mhcii_nmer(clas)
clas |
A character vector for server name |
This function takes server name "IEDB_consensusMHCII" as input into clas object.Input data for this function is present in "/data_mycobacrvR/iedb_consensus_mhcii_out" directory, therefore set working directory to "~/data_mycobacrvR/iedb_consensus_mhcii_out/" before using this function. IEDB-consensus provides epitopes of different length.
iedb_consensus_mhcii_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
Deepika Kulshreshtha
## Not run: iedb_consensus_mhcii_nmer("IEDB_consensus_mhcii") ##Conservation of all epitopes from IEDB server## Not run: iedb_consensus_mhcii_nmer("IEDB_consensus_mhcii") ##Conservation of all epitopes from IEDB server
netmhcNN_nmer is a method to conservation of epitopes among orthologs from NetMHC server 3.0 using artificial neural networks (ANNs)
netmhcNN_nmer(epi_length)netmhcNN_nmer(epi_length)
epi_length |
A character vector of epitope length |
This function takes epitope length as input into epi_length object. Input data for this function is present in "/data_mycobacrvR/netmhcNN_out" directory, therefore this directory as working directory before using this function. NetMHC server 3.0 provides epitopes by selecting window size of epitope length such as 8mer, 9mer, 10mer, 11mer. Therefore epi_length should be given as "10mer".
netmhcNN_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
Deepika Kulshreshtha
## Not run: netmhcNN_nmer("10mer") ##Conservation of 10mer epitopes from NetMHC server## Not run: netmhcNN_nmer("10mer") ##Conservation of 10mer epitopes from NetMHC server
netmhcWT_nmer is a method to conservation of epitopes among orthologs from NetMHC server 3.0 using weight matrices data
netmhcWT_nmer(epi_length)netmhcWT_nmer(epi_length)
epi_length |
A character vector of epitope length |
This function takes epitope length as input into epi_length object. Input data for this function is present in "/data_mycobacrvR/netmhcWT_out" directory, therefore set this directory as working directory before using this function. NetMHC server 3.0 provides epitopes by selecting window size of epitope length such as 8mer, 9mer, 10mer, 11mer. Therefore epi_length should be given as "10mer".
netmhcWT_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
Deepika Kulshreshtha
## Not run: netmhcWT_nmer("10mer") ##Conservation of all 10mer epitopes from NetMHC server## Not run: netmhcWT_nmer("10mer") ##Conservation of all 10mer epitopes from NetMHC server
propred_nmer is a method to conservation of epitopes among orthologs from Propred server data
propred_nmer(epi_length)propred_nmer(epi_length)
epi_length |
A character vector of epitope length |
This function takes epitope length as input into epi_length object. Input data for this function is present in "/data_mycobacrvR/propred_out" directory, therefore set this directory as working directory before using this function. Propred server provide epitopes of epitope length 9. Therefore epi_length should be given as "9mer".
propred_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
Deepika Kulshreshtha
## Not run: propred_nmer("9mer") ##Conservation of all 9mer epitopes from Propred server## Not run: propred_nmer("9mer") ##Conservation of all 9mer epitopes from Propred server