Other packages > Find by keyword >

Explore topics

By keyword . Oldest R packages . Newest R packages . Top downloaded R packages . Datasets . Archived R packages . Top downloaded last week . Top downloaded yesterday

MHCtools

Star Watch Copy Code

Analysis of MHC Data in Non-Model Species

View on CRAN: Click here

Download and install MHCtools package within the R console
Install from CRAN:

 install.packages("MHCtools")

Install from Github:

 library("remotes")

                        install_github("cran/MHCtools")

Install by package version:

 library("remotes")

                        install_version("MHCtools", "1.5.3")

Attach the package and use:

 library("MHCtools")

Maintained by
Jacob Roved
[Scholar Profile | Author Map]

All associated links for this package

First Published: 2017-09-29

Latest Update: 2023-07-08

Description:

Fifteen tools for bioinformatics processing and analysis of major histocompatibility complex (MHC) data. The functions are tailored for amplicon data sets that have been filtered using the dada2 method (for more information on dada2, visit ), but even other types of data sets can be analyzed. The ReplMatch() function matches replicates in data sets in order to evaluate genotyping success. The GetReplTable() and GetReplStats() functions perform such an evaluation. The CreateFas() function creates a fasta file with all the sequences in the data set. The CreateSamplesFas() function creates individual fasta files for each sample in the data set. The DistCalc() function calculates Grantham, Sandberg, or p-distances from pairwise comparisons of all sequences in a data set, and mean distances of all pairwise comparisons within each sample in a data set. The function additionally outputs five tables with physico-chemical z-descriptor values (based on Sandberg et al. 1998) for each amino acid position in all sequences in the data set. These tables may be useful for further downstream analyses, such as estimation of MHC supertypes. The BootKmeans() function is a wrapper for the kmeans() function of the 'stats' package, which allows for bootstrapping. Bootstrapping k-estimates may be desirable in data sets, where e.g. BIC- vs. k-values do not produce clear inflection points ("elbows"). BootKmeans() performs multiple runs of kmeans() and estimates optimal k-values based on a user-defined threshold of BIC reduction. The method is an automated and bootstrapped version of visually inspecting elbow plots of BIC- vs. k-values. The ClusterMatch() function is a tool for evaluating whether different k-means() clustering models identify similar clusters, and summarize bootstrap model stats as means for different estimated values of k. It is designed to take files produced by the BootKmeans() function as input, but other data can be analysed if the descriptions of the required data formats are observed carefully. The PapaDiv() function compares parent pairs in the data set and calculate their joint MHC diversity, taking into account sequence variants that occur in both parents. The HpltFind() function infers putative haplotypes from families in the data set. The GetHpltTable() and GetHpltStats() functions evaluate the accuracy of the haplotype inference. The CreateHpltOccTable() function creates a binary (logical) haplotype-sequence occurrence matrix from the output of HpltFind(), for easy overview of which sequences are present in which haplotypes. The HpltMatch() function compares haplotypes to help identify overlapping and potentially identical types. The NestTablesXL() function translates the output from HpltFind() to an Excel workbook, that provides a convenient overview for evaluation and curating of the inferred putative haplotypes.

How to cite:

Jacob Roved (2017). MHCtools: Analysis of MHC Data in Non-Model Species. R package version 1.5.3, https://cran.r-project.org/web/packages/MHCtools. Accessed 22 Dec. 2024.

Previous versions and publish date:

1.0.0 (2017-09-29 18:50), 1.1.0 (2017-10-23 13:49), 1.1.1 (2019-02-04 22:03), 1.2.0 (2019-08-08 18:40), 1.2.1 (2019-08-11 17:20), 1.3.0 (2020-09-16 10:10), 1.4.0 (2021-09-14 13:10), 1.4.1 (2021-10-11 13:20), 1.4.2 (2022-05-23 20:10), 1.4.3 (2022-08-15 19:40), 1.5.0 (2022-10-19 23:47), 1.5.1 (2023-03-22 17:20), 1.5.2 (2023-07-01 12:30)

Other packages that cited MHCtools R package

View MHCtools citation profile

Other R packages that MHCtools depends, imports, suggests or enhances

View MHCtools dependency map

Complete documentation for MHCtools

View documentation PDF

Functions, R codes and Examples using the MHCtools R package

Some associated functions: BootKmeans . ClusterMatch . CreateFas . CreateHpltOccTable . CreateSamplesFas . DistCalc . GetHpltStats . GetHpltTable . GetReplStats . GetReplTable . HpltFind . HpltMatch . NestTablesXL . PapaDiv . ReplMatch . hplt_occurrence_matrix . k_summary_table . nest_table . parents_table . replicates_table . sequence_table . sequence_table_fas . sequence_table_hplt . sequence_table_repl . z1_matrix . z2_matrix . z3_matrix . z4_matrix . z5_matrix .
Some associated R codes: BootKmeans_func_20210910.R . ClusterMatch_func_20210910.R . CreateFas_func_20170924.R . CreateHpltOccTable_func_20221010.R . CreateSamplesFas_func_20170924.R . DistCalc_func_20221007.R . GetHpltStats_func_20200915.R . GetHpltTable_func_20200915.R . GetReplStats_func_20200914.R . GetReplTable_func_20200914.R . HpltFind_func_20220802.R . HpltMatch_func_20221014.R . NestTablesXL_func_20221012.R . PapaDiv_func_20200915.R . ReplMatch_func_20221007.R . hplt_occurrence_matrix.R . k_summary_table.R . nest_table.R . parents_table.R . replicates_table.R . sequence_table.R . sequence_table_fas.R . sequence_table_hplt.R . sequence_table_repl.R . z1_matrix.R . z2_matrix.R . z3_matrix.R . z4_matrix.R . z5_matrix.R . Full MHCtools package functions and examples

Downloads during the last 30 days

Get rewarded with contribution points by helping add

Reviews / comments / questions /suggestions ↴↴↴

Today's Hot Picks in Authors and Packages

quickcode

Quick and Essential 'R' Tricks for Better Scripts

The NOT functions, 'R' tricks and a compilation of some simple quick plus often used 'R' codes to im ...
Download / Learn more Package Citations See dependency

Maintainer: Obinna Obianom (view profile)

tropAlgebra

Tropical Algebraic Functions

It includes functions like tropical addition, tropical multiplication for vectors and matrices. In t ...
Download / Learn more Package Citations See dependency

Maintainer: Muhammad Kashif Hanif (view profile)

composits

Compositional, Multivariate and Univariate Time Series Outlier Ensemble

A compositional multivariate and univariate time series outlier ensemble.It uses the four R packages ...
Download / Learn more Package Citations See dependency

Maintainer: Sevvandi Kandanaarachchi (view profile)

LOGANTree

Tree-Based Models for the Analysis of Log Files from Computer-Based Assessments

Enables researchers to model log-file data from computer-based assessments using machine-learning te ...
Download / Learn more Package Citations See dependency

Maintainer: Qi Qin (view profile)

Rfast2

A Collection of Efficient and Extremely Fast R Functions II

A collection of fast statistical and utility functions for data analysis. Functions for regression, ...
Download / Learn more Package Citations See dependency

Maintainer: Manos Papadakis (view profile)

dmlalg

Double Machine Learning Algorithms

Implementation of double machine learning (DML) algorithms in R, based on Emmenegger and Buehlmann ...
Download / Learn more Package Citations See dependency

Maintainer: Corinne Emmenegger (view profile)