Remove broken seqinfo links

Author: timoast

DESCRIPTION

@@ -19,7 +19,7 @@ Depends:
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 URL: https://github.com/stuart-lab/signac, https://stuartlab.org/signac
 BugReports: https://github.com/stuart-lab/signac/issues
 LinkingTo: Rcpp

R/genomeinfodb-methods.R

@@ -18,7 +18,7 @@ setOldClass(Classes = "ChromatinAssay")
 #' Access and modify sequence information for ChromatinAssay objects
 #'
 #' Methods for accessing and modifying
-#' \code{\link[GenomeInfoDb]{Seqinfo}} object information stored in a
+#' \code{Seqinfo} object information stored in a
 #' \code{\link{ChromatinAssay}} object.
 #'
 #' @name seqinfo-methods
@@ -27,7 +27,7 @@ setOldClass(Classes = "ChromatinAssay")
 #' @aliases seqinfo seqinfo,ChromatinAssay-method
 #' @seealso
 #' \itemize{
-#'   \item{\link[GenomeInfoDb]{seqinfo} in the \pkg{GenomeInfoDb} package.}
+#'   \item{seqinfo in the \pkg{GenomeInfoDb} package.}
 #'   \item{\link{ChromatinAssay-class}}
 #'  }
 #' @exportMethod seqinfo
@@ -40,7 +40,7 @@ setMethod(
   }
 )
 
-#' @param value A \code{\link[GenomeInfoDb]{Seqinfo}} object or name of a UCSC
+#' @param value A \code{Seqinfo} object or name of a UCSC
 #' genome to store in the \code{\link{ChromatinAssay}}
 #' @describeIn seqinfo-methods set method for ChromatinAssay objects
 #' @exportMethod seqinfo<-

R/objects.R

@@ -77,7 +77,7 @@ Motif <- setClass(
 #' genomic location of features in the object
 #' @slot motifs A \code{\link{Motif}} object
 #' @slot fragments A list of \code{\link{Fragment}} objects.
-#' @slot seqinfo A \code{\link[GenomeInfoDb]{Seqinfo}} object containing basic
+#' @slot seqinfo A \code{Seqinfo} object containing basic
 #' information about the genome sequence used.
 #' @slot annotation A  \code{\link[GenomicRanges]{GRanges}} object containing
 #' genomic annotations. This should be a GRanges object with the following 
@@ -152,7 +152,7 @@ ChromatinAssay <- setClass(
 #' created using the \code{\link{CreateFragmentObject}} and
 #' \code{\link{Fragments}} functions. Alternatively, a list of
 #' \code{\link{Fragment}} objects can be provided.
-#' @param genome A \code{\link[GenomeInfoDb]{Seqinfo}} object containing basic
+#' @param genome A \code{Seqinfo} object containing basic
 #' information about the genome used. Alternatively, the name of a UCSC genome
 #' can be provided and the sequence information will be downloaded from UCSC.
 #' @param annotation A set of \code{\link[GenomicRanges]{GRanges}} containing
@@ -363,7 +363,7 @@ CreateChromatinAssay <- function(
 }
 
 #' @param ranges A GRanges object
-#' @param seqinfo A \code{\link[GenomeInfoDb]{Seqinfo}} object containing basic
+#' @param seqinfo A \code{Seqinfo} object containing basic
 #' information about the genome used. Alternatively, the name of a UCSC genome
 #' can be provided and the sequence information will be downloaded from UCSC.
 #' @param annotation Genomic annotation. It must have the following columns:

R/quantification.R

@@ -127,7 +127,7 @@ AggregateTiles.default <- function(
 #' \code{\link{Fragment}} objects
 #' @param genome A vector of chromosome sizes for the genome. This is used to
 #' construct the genome bin coordinates. The can be obtained by calling
-#' \code{\link[GenomeInfoDb]{seqlengths}} on a
+#' \code{seqlengths} on a
 #' \code{\link[BSgenome]{BSgenome-class}} object.
 #' @param cells Vector of cells to include. If NULL, include all cells found
 #' in the fragments file