View source: R/Seurat.Utils.Metadata.R
addMetaFraction | R Documentation |
Add a new metadata column to a Seurat object, representing the fraction of a gene set in the transcriptome (expressed as a percentage).
addMetaFraction(
obj,
col.name = "percent.mito",
gene.symbol.pattern = c("^MT\\.|^MT-", FALSE)[1],
assay = "RNA",
layer = "data",
gene.set = FALSE,
verbose = TRUE
)
obj |
Seurat object to which the new metadata column will be added. Default: ls.Seurat[1] |
col.name |
Name of the new metadata column to be added. Default: 'percent.mito' |
gene.symbol.pattern |
Regular expression pattern to match gene symbols. Default: c("^MT\.|^MT-", FALSE)1 |
assay |
Name of the assay to be used. Default: 'RNA' |
layer |
Name of the layer to be used. Default: 'data' |
gene.set |
A set of gene symbols. If specified, it will be used instead of gene.symbol.pattern. Default: |
verbose |
Logical indicating whether to display detailed messages (TRUE) or not (FALSE). Default: |
colSums
## Not run:
if (interactive()) {
ls.Seurat[[1]] <- addMetaFraction(col.name = "percent.mito", gene.symbol.pattern = "^MT\\.|^MT-", obj = ls.Seurat[[1]])
ls.Seurat[[1]] <- addMetaFraction(col.name = "percent.ribo", gene.symbol.pattern = "^RPL|^RPS", obj = ls.Seurat[[1]])
ls.Seurat[[1]] <- addMetaFraction(col.name = "percent.AC.GenBank", gene.symbol.pattern = "^AC[0-9]{6}\\.", obj = ls.Seurat[[1]])
ls.Seurat[[1]] <- addMetaFraction(col.name = "percent.AL.EMBL", gene.symbol.pattern = "^AL[0-9]{6}\\.", obj = ls.Seurat[[1]])
ls.Seurat[[1]] <- addMetaFraction(col.name = "percent.LINC", gene.symbol.pattern = "^LINC0", obj = ls.Seurat[[1]])
ls.Seurat[[1]] <- addMetaFraction(col.name = "percent.MALAT1", gene.symbol.pattern = "^MALAT1", obj = ls.Seurat[[1]])
colnames(ls.Seurat[[1]]@meta.data)
HGA_MarkerGenes <- c(
"ENO1", "IGFBP2", "WSB1", "DDIT4", "PGK1", "BNIP3", "FAM162A", "TPI1",
"VEGFA", "PDK1", "PGAM1", "IER2", "FOS", "BTG1", "EPB41L4A-AS1", "NPAS4", "HK2", "BNIP3L",
"JUN", "ENO2", "GAPDH", "ANKRD37", "ALDOA", "GADD45G", "TXNIP"
)
sobj <- addMetaFraction(col.name = "percent.HGA", gene.set = HGA_MarkerGenes, obj = sobj)
}
## End(Not run)
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