readyomics (version 0.1.1)

add_feat_name: Append feature names to a dana object

Description

Adds a feat_name column to the dana object to map feat_id to original labels.

Usage

add_feat_name(dana_obj, feat_names)

Value

A modified version of dana_obj, with a feat_name column added to applicable components.

Arguments

dana_obj

A dana object returned by dana().

feat_names

A data frame mapping feat_id to feat_name. Must contain columns "feat_id" and "feat_name".

See Also

dana() for fitting differential analysis models on omics datasets.

Examples

set.seed(123)
mock_X <- matrix(rnorm(20 * 5), nrow = 20)
colnames(mock_X) <- paste0("feat_", seq_len(5))
rownames(mock_X) <- paste0("sample_", seq_len(20))

mock_names <- data.frame(
  feat_id = paste0("feat_", seq_len(5)),
  feat_name = c(
    "Glucose",
    "Lactic acid",
    "Citric acid",
    "Palmitic acid",
    "Cholesterol"
  ),
  stringsAsFactors = FALSE
)

sample_data <- data.frame(
  sample_id = rownames(mock_X),
  group = factor(rep(c("A", "B"), each = 10)),
  time = factor(rep(c("T1", "T2"), times = 10)),
  subject_id = factor(rep(seq_len(10), each = 2)),
  stringsAsFactors = FALSE
)
rownames(sample_data) <- sample_data$sample_id

fit_df <- data.frame(
  feat_id = rep(colnames(mock_X), each = 2),
  Coefficient = rep(c("(Intercept)", "groupB"), 5),
  Estimate = rnorm(10),
  `Pr(>|t|)` = runif(10),
  padj = runif(10),
  stringsAsFactors = FALSE
)

# Mock dana object
dana_obj <- list(
  X = mock_X,
  sdata = sample_data,
  formula_rhs = ~ group,
  fit = fit_df,
  lrt = data.frame(),
  ranef = data.frame()
)
class(dana_obj) <- "dana"

# Add fearure labels
dana_obj <- dana_obj |>
  add_feat_name(mock_names)