uniquifyFeatureNames: Make feature names unique
BIOC
scuttle: Single-Cell RNA-Seq Analysis Utilities
(e.g., Ensembl) for use as row names.
Usage
uniquifyFeatureNames(ID, names)
(e.g., Ensembl) for use as row names.
Usage
uniquifyFeatureNames(ID, names)
all.ids <- paste0("GENE", seq_along(all.genes))
out <- uniquifyFeatureNames(all.ids, all.genespassed to \code{pheatmap}.
#' @importFrom pheatmap pheatmap
#' @importFrom scater uniquifyFeatureNames#' uniquifyFeatureNames(
#' ID=paste0("ENSG0000000", 1:5),
#' names=c("A", NA, "B", "C", "A")
, perCellQCMetrics, perFeatureQCMetrics, quickPerCellQC, readSparseCounts, sumCountsAcrossCells, sumCountsAcrossFeatures, uniquifyFeatureNames
#'
#' @importFrom DropletUtils read10xCounts
#' @importFrom scater uniquifyFeatureNames
#' @export
scuttle::sumCountsAcrossFeatures
#' @export
#'
#' @importFrom DropletUtils read10xCounts
#' @importFrom scater uniquifyFeatureNames
/to/outs/")
#' }
#'
::uniquifyFeatureNames.
Genes with multiple possible symbols will be labelled as Ensembl ID.
Genes absent from OrgDb/Biomart will be labelled as Ensembl ID.
#' @importFrom scater uniquifyFeatureNames
#' @importFrom ggplot2 geom_text aes
#' @importMethodsFrom SummarizedExperiment assay
= "pbmc3k")
rownames(tenx_pbmc3k) <- uniquifyFeatureNames(rowData(tenx_pbmc3k)$ENSEMBL_ID,
rowData(tenx_pbmc3k
")
# rownames(tenx_pbmc3k) <- uniquifyFeatureNames(rowData(tenx_pbmc3k)$ENSEMBL_ID,
# rowData(tenx_pbmc3k
, uniquifyFeatureNames(ENSEMBL, SYMBOL))
# pull reduced dimensions
k <- c("tsne1", "tsne2")
"
## ----rename_rows--------------------------------------------------------------
rownames(pbmc) <- uniquifyFeatureNames(rowData(pbmc
-missing symbols:
rownames(sce.ens) <- uniquifyFeatureNames(
rownames(sce.ens), rowData(sce.ens)$originalName
<- TENxPBMCData(dataset = "pbmc3k")
rownames(tenx_pbmc3k) <- uniquifyFeatureNames(rowData(tenx_pbmc3k)$ENSEMBL_ID,
rowData
and the gene symbol. Uses scater::uniquifyFeatureNames.
#' \item Genes with multiple possible symbols will be labelled
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