Package: midasHLA 1.15.0

Maciej Migdał

midasHLA: R package for immunogenomics data handling and association analysis

MiDAS is a R package for immunogenetics data transformation and statistical analysis. MiDAS accepts input data in the form of HLA alleles and KIR types, and can transform it into biologically meaningful variables, enabling HLA amino acid fine mapping, analyses of HLA evolutionary divergence, KIR gene presence, as well as validated HLA-KIR interactions. Further, it allows comprehensive statistical association analysis workflows with phenotypes of diverse measurement scales. MiDAS closes a gap between the inference of immunogenetic variation and its efficient utilization to make relevant discoveries related to T cell, Natural Killer cell, and disease biology.

Authors:Christian Hammer [aut], Maciej Migdał [aut, cre]

midasHLA_1.15.0.tar.gz
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midasHLA.pdf |midasHLA.html✨
midasHLA/json (API)
NEWS

# Install 'midasHLA' in R:

install.packages('midasHLA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

MiDAS_tut_HLA - MiDAS tutorial HLA data
MiDAS_tut_KIR - MiDAS tutorial KIR data
MiDAS_tut_object - MiDAS tutorial MiDAS object
MiDAS_tut_pheno - MiDAS tutorial phenotype data
allele_frequencies - Alleles frequencies scraped from allelefrequencies.net
dict_dist_grantham - Grantham distance
kir_frequencies - KIR genes frequencies scraped from allelefrequencies.net

On BioConductor:midasHLA-1.13.0(bioc 3.20)midasHLA-1.12.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

cellbiology genetics statisticalmethod

4.78 score 3 scripts 196 downloads 36 exports 129 dependencies

Last updated 25 days agofrom:b204d6ff76. Checks:OK: 1 WARNING: 4 ERROR: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	WARNING	Oct 31 2024
R-4.5-linux	WARNING	Oct 30 2024
R-4.4-win	WARNING	Oct 31 2024
R-4.4-mac	ERROR	Oct 31 2024
R-4.3-win	WARNING	Oct 31 2024
R-4.3-mac	ERROR	Oct 31 2024

Exports:analyzeAssociations analyzeConditionalAssociations checkAlleleFormat checkKirGenesFormat convertAlleleToVariable countsToVariables filterByFrequency filterByOmnibusGroups filterByVariables getAAFrequencies getAlleleResolution getAllelesForAA getExperiments getFrequencies getHlaCalls getHlaFrequencies getHlaKirInteractions getKirCalls getKIRFrequencies getOmnibusGroups getPlaceholder getVariableAAPos hlaCallsGranthamDistance hlaToAAVariation hlaToVariable HWETest kableResults omnibusTest prepareMiDAS readHlaAlignments readHlaCalls readKirCalls reduceAlleleResolution reduceHlaCalls runMiDAS summariseAAPosition

Dependencies:abind askpass assertthat backports base64enc Biobase BiocBaseUtils BiocGenerics bit bit64 bitops boot broom bslib cachem chron cli clipr codetools colorspace cpp11 crayon curl data.table DelayedArray digest dplyr evaluate fansi farver fastmap fontawesome forcats foreach formattable fs generics GenomeInfoDb GenomeInfoDbData GenomicRanges glmnet glue HardyWeinberg haven highr hms htmltools htmlwidgets httr IRanges iterators jomo jquerylib jsonlite kableExtra knitr labeling lattice lifecycle lme4 magrittr MASS Matrix MatrixGenerics matrixStats memoise mice mime minqa mitml MultiAssayExperiment munsell nlme nloptr nnet numDeriv openssl ordinal pan pillar pkgconfig prettyunits progress purrr qdapTools R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl readr rlang rmarkdown rpart Rsolnp rstudioapi S4Arrays S4Vectors sass scales shape SparseArray stringi stringr SummarizedExperiment survival svglite sys systemfonts tibble tidyr tidyselect tinytex truncnorm tzdb ucminf UCSC.utils utf8 vctrs viridisLite vroom withr xfun XML xml2 XVector yaml zlibbioc

MiDAS quick start

Maciej Migdał & Christian Hammer

Rendered fromMiDAS_vignette.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2021-01-27
Started: 2020-10-20

MiDAS tutorial

Maciej Migdał & Christian Hammer

Rendered fromMiDAS_tutorial.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2021-03-30
Started: 2020-10-20

Help page	Topics
Transform amino acid variation data frame into counts table	aaVariationToCounts
Adjust P-values for Multiple Comparisons	adjustPValues
Alleles frequencies scraped from allelefrequencies.net	allele_frequencies
Association analysis	analyzeAssociations
Stepwise conditional association analysis	analyzeConditionalAssociations
Apply inheritance model	applyInheritanceModel applyInheritanceModel.matrix applyInheritanceModel.SummarizedExperiment
Coerce MiDAS to Data Frame	as.data.frame.MiDAS
Backquote character	backquote
Check if character matches one of possible values	characterMatches
Check HLA allele format	checkAlleleFormat
Assert colData data	checkColDataFormat
Assert hla calls data frame format	checkHlaCallsFormat
Assert KIR counts data frame format	checkKirCallsFormat
Check KIR genes format	checkKirGenesFormat
Assert statistical model	checkStatisticalModel
Check column names	colnamesMatches
Convert allele numbers to additional variables	convertAlleleToVariable
Convert counts table to variables	countsToVariables
Helper transform data frame to experiment matrix	dfToExperimentMat
Grantham distance	dict_dist_grantham
Calculate Grantham distance between amino acid sequences	distGrantham
Helper transform experiment matrix to data frame	experimentMatToDf
Filter MiDAS object by frequency	filterByFrequency
Filter MiDAS object by omnibus groups	filterByOmnibusGroups
Filter MiDAS object by features	filterByVariables
Filter experiment by frequency	filterExperimentByFrequency filterExperimentByFrequency.matrix filterExperimentByFrequency.SummarizedExperiment
Filter experiment by variable	filterExperimentByVariables filterExperimentByVariables.matrix filterExperimentByVariables.SummarizedExperiment
Filter list by elements	filterListByElements
Pretty format statistical analysis results helper	formatResults
Calculate amino acid frequencies	getAAFrequencies
Infer HLA allele resolution	getAlleleResolution
Get HLA alleles for amino acid position	getAllelesForAA
Calculate experiment's features frequencies	getExperimentFrequencies getExperimentFrequencies.matrix getExperimentFrequencies.SummarizedExperiment
Get experiment's population multiplicator	getExperimentPopulationMultiplicator getExperimentPopulationMultiplicator.matrix getExperimentPopulationMultiplicator.SummarizedExperiment
Get available experiments in MiDAS object.	getExperiments
Calculate features frequencies for a given experiment in MiDAS object.	getFrequencies
Helper function for filtering frequency data frame	getFrequencyMask
Get HLA calls from MiDAS object.	getHlaCalls
Get HLA calls genes	getHlaCallsGenes
Calculate HLA allele frequencies	getHlaFrequencies
Get HLA - KIR interactions	getHlaKirInteractions
Get KIR calls from MiDAS object.	getKirCalls
Calculate KIR genes frequencies	getKIRFrequencies
Get attributes of statistical model object	getObjectDetails
Get omnibus groups from MiDAS object.	getOmnibusGroups
Get placeholder name from MiDAS object.	getPlaceholder
Helper transforming reference frequencies	getReferenceFrequencies
Find variable positions in sequence alignment	getVariableAAPos
Check if tidy method for class exist	hasTidyMethod
Helper function returning alignment for Grantham distance calculations	hlaAlignmentGrantham
Calculate Grantham distance between HLA alleles	hlaCallsGranthamDistance
Transform HLA calls to counts table	hlaCallsToCounts
Generate amino acid variation matrix	hlaToAAVariation
Convert HLA calls to variables	hlaToVariable
Test for Hardy Weinberg equilibrium	HWETest
Check if object is character vector or NULL	isCharacterOrNULL
Check if object is of class x	isClass
Check if object is of class x or null	isClassOrNULL
Check if object is count or NULL	isCountOrNULL
Check if vector contains only counts or zeros	isCountsOrZeros
Check if frequencies can be calculated for an experiment	isExperimentCountsOrZeros
Check if experiment is inheritance model applicable	isExperimentInheritanceModelApplicable isExperimentInheritanceModelApplicable.matrix isExperimentInheritanceModelApplicable.SummarizedExperiment
Check if object is flag or NULL	isFlagOrNULL
Check if object is number or NULL	isNumberOrNULL
Check if object is string or NULL	isStringOrNULL
Check if object is TRUE or FALSE flag	isTRUEorFALSE
Iterative likelihood ratio test	iterativeLRT
Iteratively evaluate model for different variables	iterativeModel
Create association analysis results table in HTML or LaTeX	kableResults
KIR genes frequencies scraped from allelefrequencies.net	kir_frequencies
lapply with tryCatch routine	lapply_tryCatch
List HLA alleles dictionaries	listMiDASDictionaries
Likelihood ratio test	LRTest
MiDAS tutorial HLA data	MiDAS_tut_HLA
MiDAS tutorial KIR data	MiDAS_tut_KIR
MiDAS tutorial MiDAS object	MiDAS_tut_object
MiDAS tutorial phenotype data	MiDAS_tut_pheno
MiDAS class	filterByFrequency,MiDAS-method filterByOmnibusGroups,MiDAS-method filterByVariables,MiDAS-method getAllelesForAA,MiDAS-method getExperiments,MiDAS-method getFrequencies,MiDAS-method getHlaCalls,MiDAS-method getKirCalls,MiDAS-method getOmnibusGroups,MiDAS-method getPlaceholder,MiDAS-method MiDAS MiDAS-class
Transform MiDAS to wide format data.frame	midasToWide
Check if placeholder is present in object formula	objectHasPlaceholder
Omnibus test	omnibusTest
Construct a MiDAS object	prepareMiDAS
Prepare MiDAS data on HLA amino acid level	prepareMiDAS_hla_aa
Prepare MiDAS data on HLA allele level	prepareMiDAS_hla_alleles
Prepare MiDAS data on custom HLA level	prepareMiDAS_hla_custom
Prepare MiDAS data on HLA divergence level	prepareMiDAS_hla_divergence
Prepare MiDAS data on HLA allele's G groups level	prepareMiDAS_hla_g_groups
Prepare MiDAS data on HLA heterozygosity level	prepareMiDAS_hla_het
Prepare MiDAS data on HLA - KIR interactions level	prepareMiDAS_hla_kir_interactions
Prepare MiDAS data on HLA allele's groups level	prepareMiDAS_hla_NK_ligands
Prepare MiDAS data on HLA allele's supertypes level	prepareMiDAS_hla_supertypes
Prepare MiDAS data on custom KIR level	prepareMiDAS_kir_custom
Prepare MiDAS data on KIR genes level	prepareMiDAS_kir_genes
Prepare MiDAS data on KIR haplotypes level	prepareMiDAS_kir_haplotypes
Read HLA allele alignments	readHlaAlignments
Read HLA allele calls	readHlaCalls
Read KIR calls	readKirCalls
Reduce HLA alleles	reduceAlleleResolution
Reduce HLA calls resolution	reduceHlaCalls
Run MiDAS statistical analysis	runMiDAS
Get variables frequencies from MiDAS	runMiDASGetVarsFreq
Check if string matches one of possible values	stringMatches
Summarize amino acid position	summariseAAPosition
Extend and Re-fit a Model Call	updateModel
Validate frequency cutoffs	validateFrequencyCutoffs

Package: midasHLA 1.15.0

midasHLA: R package for immunogenomics data handling and association analysis

MiDAS quick start

MiDAS tutorial

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)