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Convert Data to BulkPhyloExpressionSet

Source: R/phyloset_bulk.R
as_BulkPhyloExpressionSet.Rd

Convert a data frame with phylostratum, gene ID, and expression data into a BulkPhyloExpressionSet object.

Usage

as_BulkPhyloExpressionSet(
  data,
  groups = colnames(data[, 3:ncol(data)]),
  name = deparse(substitute(data)),
  strata_legend = NULL,
  ...
)

Arguments

data

A data frame where column 1 contains phylostratum information, column 2 contains gene IDs, and columns 3+ contain expression data

groups

A factor or character vector indicating which group each sample belongs to. Default uses column names from expression data

name

A character string naming the dataset. Default uses the variable name

strata_legend

A data frame with two columns: phylostratum assignments and name of each stratum. If NULL, no labels will be added (default: NULL) If NULL, uses sorted unique values from column 1

...

Additional arguments passed to BulkPhyloExpressionSet constructor

Value

A BulkPhyloExpressionSet object

Examples

# Convert data frame to BulkPhyloExpressionSet
# bulk_set <- as_BulkPhyloExpressionSet(my_data, 
#                                      groups = c("stage1", "stage1", "stage2", "stage2"),
#                                      name = "Development Dataset")