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Fixing function %||% not being found #134

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Fixing function %||% not being found #134

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9d3328b
Update RunHarmony.R
PelzKo Jul 19, 2021
1d3ad62
Update RunHarmony.R
PelzKo Jul 19, 2021
1c8d668
Update RunHarmony.R
PelzKo Jul 20, 2021
4488214
Update RunHarmony.R
PelzKo Jul 20, 2021
5ca2f1f
ran roxigenize()
PelzKo Jul 22, 2021
1d1a2a1
resolve checking failure
PelzKo Jul 22, 2021
7cdd175
Delete .Rhistory
PelzKo Sep 6, 2021
6d8737c
Update DESCRIPTION
grst Sep 6, 2021
ed84274
Merge pull request #1 from grst/patch-1
PelzKo Sep 6, 2021
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1 change: 1 addition & 0 deletions DESCRIPTION
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Expand Up @@ -23,6 +23,7 @@ RoxygenNote: 7.1.1
Depends: R(>= 3.4.0), Rcpp
LazyData: true
LinkingTo: Rcpp, RcppArmadillo, RcppProgress
biocViews:
Imports:
dplyr,
cowplot,
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1 change: 1 addition & 0 deletions NAMESPACE
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Expand Up @@ -14,4 +14,5 @@ importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(rlang,.data)
importFrom(rlang,`%||%`)
useDynLib(harmony)
4 changes: 3 additions & 1 deletion R/RunHarmony.R
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Expand Up @@ -44,6 +44,7 @@
#'
#'
#' @rdname RunHarmony
#' @importFrom rlang `%||%`
#' @export
RunHarmony <- function(object, group.by.vars, ...) {
UseMethod("RunHarmony")
Expand All @@ -57,6 +58,7 @@ RunHarmony <- function(object, group.by.vars, ...) {
#' @return Seurat (version 3) object. Harmony dimensions placed into
#' dimensional reduction object harmony. For downstream Seurat analyses,
#' use reduction='harmony'.
#' @importFrom rlang `%||%`
#' @export
RunHarmony.Seurat <- function(
object,
Expand All @@ -81,7 +83,7 @@ RunHarmony.Seurat <- function(
project.dim = TRUE,
...
) {
assay.use <- assay.use %||% DefaultAssay(object)
assay.use <- assay.use %||% Seurat::DefaultAssay(object)
if (reduction == "pca") {
tryCatch(
embedding <- Seurat::Embeddings(object, reduction = "pca"),
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21 changes: 10 additions & 11 deletions man/RunHarmony.Rd
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4 changes: 2 additions & 2 deletions man/harmony.Rd
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5 changes: 5 additions & 0 deletions src/RcppExports.cpp
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Expand Up @@ -7,6 +7,11 @@

using namespace Rcpp;

#ifdef RCPP_USE_GLOBAL_ROSTREAM
Rcpp::Rostream<true>& Rcpp::Rcout = Rcpp::Rcpp_cout_get();
Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
#endif

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@grst grst Sep 6, 2021

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Where does this change come from? Has it been added by roxygen?

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@PelzKo PelzKo Sep 6, 2021

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yes, it has. I am unsure whether it is necessary though

// compute_Y
MATTYPE compute_Y(const MATTYPE& Z_cos, const MATTYPE& R);
RcppExport SEXP _harmony_compute_Y(SEXP Z_cosSEXP, SEXP RSEXP) {
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