R/Repitope.R

In masato-ogishi/Repitope: Epitope immunogenicity prediction through in silico TCR-peptide contact potential profiling

#' Repitope: Epitope immunogenicity prediction via TCR-peptide contact potential profiling
#'
#' In silico screening of immunogenic epitopes among the vast amount of MHC-loaded peptides is a critical step toward effective precision immunotherapy. Although various sequence-based prediction models have been proposed, none of them has ever achieved meaningful accuracy and robustness. Here, we developped a framework that enables accurate classification of immunogenic epitopes and non-immunogenic MHC ligands.
#'
#' @name Repitope
#' @docType package
#' @aliases Repitope package-Repitope
#' @importFrom BBmisc chunk
#' @importFrom Biostrings AAStringSet
#' @importFrom Biostrings AA_STANDARD
#' @importFrom Biostrings mismatchTable
#' @importFrom Biostrings pairwiseAlignment
#' @importFrom Biostrings reverse
#' @importFrom car vif
#' @importFrom caret createDataPartition
#' @importFrom caret findCorrelation
#' @importFrom caret lift
#' @importFrom caret preProcess
#' @importFrom caret predictors
#' @importFrom caret rfFuncs
#' @importFrom caret rfSBF
#' @importFrom caret rfe
#' @importFrom caret rfeControl
#' @importFrom caret sbf
#' @importFrom caret sbfControl
#' @importFrom cvAUC ci.cvAUC
#' @importFrom data.table :=
#' @importFrom data.table CJ
#' @importFrom data.table as.data.table
#' @importFrom data.table copy
#' @importFrom data.table data.table
#' @importFrom data.table dcast.data.table
#' @importFrom data.table fread
#' @importFrom data.table melt.data.table
#' @importFrom data.table rbindlist
#' @importFrom data.table setcolorder
#' @importFrom data.table setkeyv
#' @importFrom data.table setorder
#' @importFrom data.table transpose
#' @importFrom DescTools Sort
#' @importFrom doParallel registerDoParallel
#' @importFrom doParallel stopImplicitCluster
#' @importFrom doSNOW registerDoSNOW
#' @importFrom dplyr %>%
#' @importFrom dplyr arrange
#' @importFrom dplyr bind_cols
#' @importFrom dplyr bind_rows
#' @importFrom dplyr distinct
#' @importFrom dplyr filter
#' @importFrom dplyr full_join
#' @importFrom dplyr group_by
#' @importFrom dplyr if_else
#' @importFrom dplyr inner_join
#' @importFrom dplyr last
#' @importFrom dplyr left_join
#' @importFrom dplyr matches
#' @importFrom dplyr mutate
#' @importFrom dplyr n_distinct
#' @importFrom dplyr nth
#' @importFrom dplyr one_of
#' @importFrom dplyr rename
#' @importFrom dplyr right_join
#' @importFrom dplyr select
#' @importFrom dplyr slice
#' @importFrom dplyr summarise
#' @importFrom dplyr tibble
#' @importFrom dplyr transmute
#' @importFrom extraTrees extraTrees
#' @importFrom foreach %do%
#' @importFrom foreach %dopar%
#' @importFrom foreach foreach
#' @importFrom fst read.fst
#' @importFrom fst read_fst
#' @importFrom fst write.fst
#' @importFrom fst write_fst
#' @importFrom ggpubr ggarrange
#' @importFrom ggpubr ggscatter
#' @importFrom ggpubr ggtexttable
#' @importFrom ggpubr rremove
#' @importFrom ggpubr theme_pubr
#' @importFrom ggpubr ttheme
#' @importFrom ggsci pal_d3
#' @importFrom grDevices colorRamp
#' @importFrom grDevices dev.off
#' @importFrom grDevices recordPlot
#' @importFrom grDevices rgb
#' @importFrom graphics text
#' @importFrom grid grid.draw
#' @importFrom gridExtra tableGrob
#' @importFrom gridExtra ttheme_minimal
#' @importFrom igraph E
#' @importFrom igraph V
#' @importFrom igraph as_edgelist
#' @importFrom igraph cluster_walktrap
#' @importFrom igraph graph_from_adjacency_matrix
#' @importFrom igraph graph_from_data_frame
#' @importFrom igraph induced_subgraph
#' @importFrom igraph layout_nicely
#' @importFrom igraph set_vertex_attr
#' @importFrom igraph simplify
#' @importFrom magrittr set_colnames
#' @importFrom magrittr set_names
#' @importFrom magrittr set_rownames
#' @importFrom MASS stepAIC
#' @importFrom Matrix forceSymmetric
#' @importFrom Matrix sparseMatrix
#' @importFrom Matrix t
#' @importFrom matrixStats rowMaxs
#' @importFrom matrixStats rowMeans2
#' @importFrom matrixStats rowMedians
#' @importFrom matrixStats rowMins
#' @importFrom mlr generateFilterValuesData
#' @importFrom mlr getTaskTargets
#' @importFrom mlr makeClassifTask
#' @importFrom msa msaClustalW
#' @importFrom msa msaConsensusSequence
#' @importFrom parallel clusterEvalQ
#' @importFrom parallel clusterExport
#' @importFrom parallel detectCores
#' @importFrom parallel makeCluster
#' @importFrom parallel splitIndices
#' @importFrom parallel stopCluster
#' @importFrom pbapply pbapply
#' @importFrom pbapply pblapply
#' @importFrom pbapply setTimerProgressBar
#' @importFrom pbapply timerProgressBar
#' @importFrom precrec evalmod
#' @importFrom pROC roc
#' @importFrom pROC ci.auc
#' @importFrom psych describe
#' @importFrom purrr flatten
#' @importFrom purrr is_empty
#' @importFrom RColorBrewer brewer.pal
#' @importFrom readr read_csv
#' @importFrom readr read_delim
#' @importFrom readr write_csv
#' @importFrom readr write_delim
#' @importFrom rlang enquo
#' @importFrom rlang eval_tidy
#' @importFrom S4Vectors nchar
#' @importFrom scales alpha
#' @importFrom scales comma
#' @importFrom scales rescale
#' @importFrom seqinr write.fasta
#' @importFrom snow clusterSetupRNGstream
#' @importFrom stats approx
#' @importFrom stats as.formula
#' @importFrom stats complete.cases
#' @importFrom stats cor
#' @importFrom stats cov2cor
#' @importFrom stats density
#' @importFrom stats lm
#' @importFrom stats median
#' @importFrom stats pchisq
#' @importFrom stats pf
#' @importFrom stats predict
#' @importFrom stats qbeta
#' @importFrom stats sd
#' @importFrom stats setNames
#' @importFrom stats weighted.mean
#' @importFrom stringdist stringdist
#' @importFrom stringi stri_reverse
#' @importFrom stringr fixed
#' @importFrom stringr str_detect
#' @importFrom stringr str_locate
#' @importFrom stringr str_remove_all
#' @importFrom stringr str_replace_all
#' @importFrom stringr str_split
#' @importFrom stringr str_sub
#' @importFrom survival Surv
#' @importFrom survival survdiff
#' @importFrom survival survfit
#' @importFrom survminer ggsurvplot
#' @importFrom tidyr crossing
#' @importFrom tidyr drop_na
#' @importFrom tidyr gather
#' @importFrom tidyr nest
#' @importFrom tidyr replace_na
#' @importFrom tidyr spread
#' @importFrom tidyr unite
#' @importFrom utils combn
#' @importFrom utils modifyList
#' @importFrom utils write.table
#' @importFrom VennDiagram venn.diagram
#' @importFrom zoo coredata
#' @import ggplot2
#' @import Peptides
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