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)
and valid (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.genesall.ids <- paste0("GENE", seq_along(all.genes))
out <- uniquifyFeatureNames(all.ids, all.genes#' uniquifyFeatureNames(
#' ID=paste0("ENSG0000000", 1:5),
#' names=c("A", NA, "B", "C", "A")
passed 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
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