| Type: | Package |
| Title: | Integrative Immunoinformatics for Mycobacterial Diseases in R Platform |
| Version: | 1.1 |
| Date: | 2022-05-12 |
| Author: | Deepika Kulshreshtha, Rupanjali Chaudhuri, Surabhi Seth, S. Ramachandran |
| Maintainer: | S. Ramachandran<ramu@igib.in> |
| 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. |
| URL: | https://mycobacteriarv.igib.res.in/download.html |
| Depends: | R (≥ 2.15), methods |
| Collate: | 'iedb_consensus_mhci_nmer.R' 'abcpred_nmer.R' 'algpred.R' 'allermatch.R' 'bcepred_nmer.R' 'bimas_nmer.R' 'filter.firstlayer.R' 'iedb_arb_mhcii_nmer.R' 'iedb_consensus_mhcii_nmer.R' 'netmhcNN_nmer.R' 'netmhcWT_nmer.R' 'propred_nmer.R' 'iedb_arb_mhci_nmer.R' 'zzz.R' |
| License: | GPL-2 |
| NeedsCompilation: | no |
| Packaged: | 2022-05-13 09:32:12 UTC; sramachandran |
| Repository: | CRAN |
| Date/Publication: | 2022-05-13 14:30:02 UTC |
Epitope conservation prediction from ABCpred server information
Description
abcpred_nmer is a method to predict conservation of epitopes among orthologs from ABCPred server data
Usage
abcpred_nmer(epi_length)Arguments
epi_length |
A character vector of epitope length |
Details
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".
Value
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
Author(s)
Deepika Kulshreshtha
Examples
## Not run: abcpred_nmer("10mer")
##Conservation of all 10mer epitopes from ABCPred serverFilter Allergic/Non Allergic proteins using output of Algpred
Description
algpred is a function to filter allergic and non allergic proteins of an organism using output of Algpred
Usage
algpred(data, organism, ginumber, prediction)Arguments
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" |
Details
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
Value
A file of filtered proteins named "filtered_algpred.txt" using the given arguments.
Author(s)
Deepika Kulshreshtha
See Also
Examples
## Not run: algpred("Final_algpred.txt",organism="Mycobacterium avium 104")Filter Allergic/Non Allergic proteins using output of Allermatch
Description
allermatch is a function to filter allergic and non allergic proteins of an organism using output of Allermatch
Usage
allermatch(data, organism, ginumber, prediction)Arguments
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" |
Details
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
Value
A file of filtered proteins named "filtered_allermatch.txt" using the given arguments.
Author(s)
Deepika Kulshreshtha
See Also
Examples
## Not run: allermatch("Final_allermatch.txt",organism="Mycobacterium avium 104")Epitope conservation prediction from Bcepred server information
Description
bcepred_nmer is a method to predict conservation of epitopes among orthologs from Bcepred server data
Usage
bcepred_nmer(clas)Arguments
clas |
A character vector for server name |
Details
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.
Value
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
Author(s)
Deepika Kulshreshtha
Examples
## Not run: bcepred_nmer("bcepred")##Conservation of epitopes from Bcepred serverEpitope prediction from Bimas server information
Description
bimas_nmer is a method to predict conservation of epitopes among orthologs from Bimas server data
Usage
bimas_nmer(epi_length)Arguments
epi_length |
A character vector of epitope length |
Details
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".
Value
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
Author(s)
Deepika Kulshreshtha
Examples
## Not run: bimas_nmer("10mer")
##Conservation of 10mer epitopes from Bimas serverFilter first layer data
Description
filter.firstlayer is a function to filter first layer data
Usage
filter.firstlayer(data, organism, ginumber, spaanscore,
subcelllocal, tmhelices, Hrefhits)
Arguments
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 |
Details
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"
Value
A file of filtered proteins named "filtered_firstlayer.txt" using the given arguments
Author(s)
Deepika Kulshreshtha, Rupanjali Chaudhuri, S. Ramachandran
Examples
## Not run: filter.firstlayer("firstlayer.txt",organism="Mycobacterium avium 104")Epitope conservation prediction for MHCI using IEDB-ARB server information
Description
iedb_arb_mhci_nmer is a method to predict conservation of epitopes among orthologs for MHCI using IEDB-ARB server data
Usage
iedb_arb_mhci_nmer(clas)Arguments
clas |
A character vector for server name |
Details
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.
Value
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
Author(s)
Deepika Kulshreshtha
Examples
## Not run: iedb_arb_mhci_nmer("IEDB_arb_mhci")
##Conservation of all epitopes from IEDB serverEpitope conservation prediction for MHCII using IEDB-ARB server information
Description
iedb_arb_mhcii_nmer is a method to predict conservation of epitopes among orthologs for MHCII using IEDB-ARB server data
Usage
iedb_arb_mhcii_nmer(clas)Arguments
clas |
A character vector for server name |
Details
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.
Value
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
Author(s)
Deepika Kulshreshtha
Examples
## Not run: iedb_arb_mhcii_nmer("IEDB_arb_mhcii")
##Conservation of all epitopes from IEDB serverEpitope 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 |
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".
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
Author(s)
Deepika Kulshreshtha
Examples
## Not run: iedb_consensus_mhci_nmer("IEDB_consensus_mhci")
##Conservation of epitopes from IEDB serverEpitope conservation prediction for MHCII using IEDB-consensus information
Description
iedb_consensus_mhcii_nmer is a method to predict conservation of epitopes among orthologs for MHCII using IEDB-consensus server data
Usage
iedb_consensus_mhcii_nmer(clas)Arguments
clas |
A character vector for server name |
Details
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.
Value
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
Author(s)
Deepika Kulshreshtha
Examples
## Not run: iedb_consensus_mhcii_nmer("IEDB_consensus_mhcii")
##Conservation of all epitopes from IEDB serverEpitope conservation prediction from NetMHC server 3.0 using artificial neural networks (ANNs)
Description
netmhcNN_nmer is a method to conservation of epitopes among orthologs from NetMHC server 3.0 using artificial neural networks (ANNs)
Usage
netmhcNN_nmer(epi_length)Arguments
epi_length |
A character vector of epitope length |
Details
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".
Value
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
Author(s)
Deepika Kulshreshtha
Examples
## Not run: netmhcNN_nmer("10mer")
##Conservation of 10mer epitopes from NetMHC serverEpitope conservation prediction from NetMHC server 3.0 using weight matrices
Description
netmhcWT_nmer is a method to conservation of epitopes among orthologs from NetMHC server 3.0 using weight matrices data
Usage
netmhcWT_nmer(epi_length)Arguments
epi_length |
A character vector of epitope length |
Details
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".
Value
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
Author(s)
Deepika Kulshreshtha
Examples
## Not run: netmhcWT_nmer("10mer")
##Conservation of all 10mer epitopes from NetMHC serverEpitope conservation prediction from Propred server information
Description
propred_nmer is a method to conservation of epitopes among orthologs from Propred server data
Usage
propred_nmer(epi_length)Arguments
epi_length |
A character vector of epitope length |
Details
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".
Value
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
Author(s)
Deepika Kulshreshtha
Examples
## Not run: propred_nmer("9mer")
##Conservation of all 9mer epitopes from Propred server