R/chromswitch.R

In selinj/chromswitch: An R package to detect chromatin state switches from epigenomic data

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# Package documentation and package-level imports
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#' chromswitch: An R package for detecting chromatin state switches
#'
#' chromswitch implements a flexible method to detect chromatin state
#' switches between samples in two biological conditions in a specific genomic
#' region of interest given peaks called from ChIP-seq data.
#'
#' @docType package
#' @name chromswitch
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#' @import methods GenomicRanges IRanges tidyr
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#' @importFrom BiocParallel bplapply bpmapply bpparam
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#' @importFrom magrittr %>%
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#' @importFrom rtracklayer import
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#' @importFrom S4Vectors isEmpty
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#' @importFrom Biobase samples
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#' @importFrom cluster silhouette
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#' @importFrom stats hclust dist cutree
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#' @importClassesFrom GenomicRanges GRanges GRangesList
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## Handle R CMD check NOTE re: the .'s that appear in pipelines
## and other undefined variables in tidyr/dplyr functions
## as per https://stackoverflow.com/a/12429344
if(getRversion() >= "2.15.1") utils::globalVariables(c(".", "Var1", "Var2",
                                                        "Freq", "Cluster",
                                                        "Condition", "Sample",
                                                        "C1", "C2", "k",
                                                        "Average_Silhouette",
                                                        "olap",
                                                        "ARI", "NMI",
                                                        "Completeness",
                                                        "Homogeneity",
                                                        "Purity", "Entropy",
                                                        "V_measure"))