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Get genomically-ordered gene position table

GetGeneOrder.Rd

Returns a data.frame of gene positions sorted by chromosome then start position, suitable for direct use as the gene_order_file argument in infercnv::CreateInfercnvObject().

Usage

GetGeneOrder(
  seurat_object,
  chromosomes = NULL,
  gene_biotype = "protein_coding",
  assay = NULL,
  chr_prefix = "chr"
)

Arguments

seurat_object

A Seurat object with feature annotations from AnnotateFeatures().

chromosomes

Numeric or character vector of chromosomes to include, e.g. 1:19 for autosomes. NULL includes all annotated chromosomes.

gene_biotype

Character. Biotype filter applied before building the table. Default "protein_coding".

assay

Character. Assay to use.

chr_prefix

Character. Prefix prepended to chromosome numbers in the output (e.g. "chr" → "chr1"). Default "chr".

Value

A data.frame with columns chr, start, end and gene symbols as rownames, sorted genomically.

See also

AnnotateFeatures(), GetFeatures()