Add annotations to SingleSampNiche genes

Adds new columns to the gene data in SingleSampNiche objects.

Usage

AddSSNicheGenes(STID_obj, ...)

# S3 method for class 'STID'
AddSSNicheGenes(
  STID_obj = NULL,
  gene = NULL,
  label = NULL,
  add_colnm = NULL,
  loop_id = "LoopAllSamp",
  niche_key = NULL,
  ...
)

Arguments

STID_obj

An STID object

...

Additional arguments passed to methods

gene

Character vector, gene names to annotate

label

Character vector, labels to assign to genes (optional)

add_colnm

Character, name of new column to add

loop_id

Character vector, sample identifiers

niche_key

Character, niche key to modify

Value

Modified STID object with updated niche gene data

Examples

if (FALSE) { # \dontrun{
# Add gene family annotations
STID_obj <- AddSSNicheGenes(ist_obj,
                           gene = c("gene1", "gene2", "gene3"),
                           label = c("toxin", "toxin", "adhesin"),
                           add_colnm = "gene_family",
                           niche_key = "niche_virulence")
} # }