diff --git a/DESCRIPTION b/DESCRIPTION index 5f9ff48..3ffadc4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: extraChIPs -Version: 1.7.2 +Version: 1.7.3 Title: Additional functions for working with ChIP-Seq data Authors@R: person("Stephen", "Pederson", email = "stephen.pederson.au@gmail.com", diff --git a/R/AllGenerics.R b/R/AllGenerics.R index 1599f0e..5776486 100644 --- a/R/AllGenerics.R +++ b/R/AllGenerics.R @@ -67,6 +67,4 @@ setGeneric( #' @export #' @name plotOverlaps #' @rdname plotOverlaps-methods -setGeneric( - 'plotOverlaps', function(x, ...) standardGeneric('plotOverlaps') -) +setGeneric('plotOverlaps', function(x, ...) standardGeneric('plotOverlaps')) diff --git a/R/addDiffStatus.R b/R/addDiffStatus.R index 93d3a2a..08bf0e6 100644 --- a/R/addDiffStatus.R +++ b/R/addDiffStatus.R @@ -39,9 +39,7 @@ #' @rdname addDiffStatus-methods #' @export #' -setGeneric( - "addDiffStatus", function(x, ...){standardGeneric("addDiffStatus")} -) +setGeneric("addDiffStatus", function(x, ...) standardGeneric("addDiffStatus")) #' @importFrom dplyr case_when #' @rdname addDiffStatus-methods #' @export diff --git a/R/fitAssayDiff.R b/R/fitAssayDiff.R index 4310969..d1fffc5 100644 --- a/R/fitAssayDiff.R +++ b/R/fitAssayDiff.R @@ -95,9 +95,7 @@ #' @rdname fitAssayDiff-methods #' @export #' -setGeneric( - "fitAssayDiff", function(x, ...){standardGeneric("fitAssayDiff")} -) +setGeneric("fitAssayDiff", function(x, ...) standardGeneric("fitAssayDiff")) #' @import SummarizedExperiment #' @importFrom edgeR glmTreat topTags glmQLFTest #' @importFrom limma eBayes treat topTable topTreat diff --git a/R/mergeByCol.R b/R/mergeByCol.R index 5d6035b..2e10b6f 100644 --- a/R/mergeByCol.R +++ b/R/mergeByCol.R @@ -62,10 +62,7 @@ #' @rdname mergeByCol-methods #' @export #' -setGeneric( - "mergeByCol", - function(x, ...){standardGeneric("mergeByCol")} -) +setGeneric("mergeByCol", function(x, ...) standardGeneric("mergeByCol")) #' @importClassesFrom S4Vectors HitsList #' @importFrom GenomeInfoDb seqinfo seqinfo<- #' @importFrom S4Vectors subjectHits queryHits mcols<- mcols diff --git a/R/mergeByHMP.R b/R/mergeByHMP.R index 049a9d6..cc9c98f 100644 --- a/R/mergeByHMP.R +++ b/R/mergeByHMP.R @@ -72,10 +72,7 @@ #' @name mergeByHMP #' @rdname mergeByHMP-methods #' @export -setGeneric( - "mergeByHMP", - function(x, ...){standardGeneric("mergeByHMP")} -) +setGeneric("mergeByHMP", function(x, ...) standardGeneric("mergeByHMP")) #' @importFrom S4Vectors DataFrame mcols mcols<- subjectHits #' @importFrom dplyr group_by summarise arrange distinct left_join bind_rows #' @importFrom dplyr across diff --git a/R/mergeBySig.R b/R/mergeBySig.R index 8224f5f..b2c7b61 100644 --- a/R/mergeBySig.R +++ b/R/mergeBySig.R @@ -55,10 +55,7 @@ #' @name mergeBySig #' @rdname mergeBySig-methods #' @export -setGeneric( - "mergeBySig", - function(x, ...){standardGeneric("mergeBySig")} -) +setGeneric("mergeBySig", function(x, ...) standardGeneric("mergeBySig")) #' @importFrom S4Vectors DataFrame mcols mcols<- #' @import GenomicRanges #' @rdname mergeBySig-methods diff --git a/R/plotAssayDensities.R b/R/plotAssayDensities.R index a547ee0..2a8086d 100644 --- a/R/plotAssayDensities.R +++ b/R/plotAssayDensities.R @@ -38,8 +38,7 @@ #' @export #' setGeneric( - "plotAssayDensities", - function(x, ...){standardGeneric("plotAssayDensities")} + "plotAssayDensities", function(x, ...) standardGeneric("plotAssayDensities") ) #' @import SummarizedExperiment #' @importFrom stats density diff --git a/R/plotAssayHeatmap.R b/R/plotAssayHeatmap.R index a1f604a..2775f35 100644 --- a/R/plotAssayHeatmap.R +++ b/R/plotAssayHeatmap.R @@ -58,8 +58,7 @@ #' @export #' setGeneric( - "plotAssayHeatmap", - function(x, ...){standardGeneric("plotAssayHeatmap")} + "plotAssayHeatmap", function(x, ...) standardGeneric("plotAssayHeatmap") ) #' #' @import SummarizedExperiment diff --git a/R/plotAssayPCA.R b/R/plotAssayPCA.R index 809ad65..edebabc 100644 --- a/R/plotAssayPCA.R +++ b/R/plotAssayPCA.R @@ -47,10 +47,7 @@ #' @rdname plotAssayPCA-methods #' @export #' -setGeneric( - "plotAssayPCA", - function(x, ...){standardGeneric("plotAssayPCA")} -) +setGeneric("plotAssayPCA", function(x, ...) standardGeneric("plotAssayPCA")) #' @import SummarizedExperiment #' @importFrom broom tidy #' @importFrom dplyr left_join diff --git a/R/plotAssayRle.R b/R/plotAssayRle.R index a7f22a1..28f40d1 100644 --- a/R/plotAssayRle.R +++ b/R/plotAssayRle.R @@ -19,7 +19,7 @@ #' @param by_x Boxplots will be drawn by this grouping variable from #' `colData(x)`. If not specified, the default values will be `colnames(x)` #' @param n_max Maximum number of points to plot -#' @param trans character(1). NUuerical transformation to apply to the data +#' @param trans character(1). Numerical transformation to apply to the data #' prior to RLE calculation #' @param ... Passed to \link[ggplot2]{geom_boxplot} #' diff --git a/R/plotProfileHeatmap.R b/R/plotProfileHeatmap.R index 42f20a3..911e830 100644 --- a/R/plotProfileHeatmap.R +++ b/R/plotProfileHeatmap.R @@ -97,8 +97,7 @@ setGeneric( #' @importFrom rlang ensym #' @export setMethod( - "plotProfileHeatmap", - signature = signature(object = "GenomicRangesList"), + "plotProfileHeatmap", signature = signature(object = "GenomicRangesList"), function( object, profileCol = "profile_data", xValue = "bp", fillValue = "score", @@ -154,8 +153,7 @@ setMethod( #' @rdname plotProfileHeatmap-methods #' @export setMethod( - "plotProfileHeatmap", - signature = signature(object = "GenomicRanges"), + "plotProfileHeatmap", signature = signature(object = "GenomicRanges"), function( object, profileCol = "profile_data", xValue = "bp", fillValue = "score", diff --git a/man/plotAssayRle-methods.Rd b/man/plotAssayRle-methods.Rd index f6b978c..5db147c 100644 --- a/man/plotAssayRle-methods.Rd +++ b/man/plotAssayRle-methods.Rd @@ -38,7 +38,7 @@ Commonly an alternative sample label.} \item{n_max}{Maximum number of points to plot} -\item{trans}{character(1). NUuerical transformation to apply to the data +\item{trans}{character(1). Numerical transformation to apply to the data prior to RLE calculation} } \value{