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Run tAge pipeline separately per group factor (e.g., "tissue")

Source: R/predict.R
tAge_by_group.Rd

Preprocesses every level of split_by on its own – gene filtering, normalisation and reference centring all happen within the stratum, as the clocks were trained and applied in the paper – and predicts on the combined data. This is tAge_preprocessing with split_by followed by predict_tAge.

Usage

tAge_by_group(
  eset,
  split_by,
  model_paths,
  species = "mouse",
  mode = NULL,
  control_group_column = NULL,
  control_group_label = NULL,
  count_threshold = 10,
  percent_threshold = 20,
  min_samples = 5,
  verbose = TRUE,
  gene_mapping_type = "auto",
  return_std = NULL,
  age_units = c("auto", "months", "years"),
  normalized_age = c("fraction", "percent")
)

Arguments

eset

An ExpressionSet, e.g. from pseudobulk aggregation.

split_by

Character. Column in pData to split by (e.g., "tissue").

model_paths

Clock table with a path column, or named list of model paths; see predict_tAge.

species

Species of the samples: "mouse", "rat", "human" or "monkey" (see tage_species). Default is "mouse".

mode

"EN" or "BR". Default NULL takes each model's type from the clock table, the registry or its file name.

control_group_column

Character string specifying the column name in phenoData that contains control group labels. Default is NULL.

control_group_label

Character string specifying the label for control samples. Default is NULL. With split_by, the controls of each stratum are its reference; a stratum without controls is centred on all of its samples, with a warning. A column that does not exist, or a label that no sample carries, is an error.

count_threshold

Numeric threshold for minimum expression count in gene filtering. Default is 10.

percent_threshold

Numeric threshold for minimum percentage of samples that must have expression above count_threshold. Default is 20.

min_samples

Integer. Strata with fewer samples are left out, with a warning. Default 5.

verbose

Logical indicating whether to print progress messages. Default is TRUE.

gene_mapping_type

Identifier type of the row names: "Ensembl", "Gene.Symbol", "Entrez" or "auto" (default, detected from the gene table; see map_genes).

return_std

Logical. Whether to keep the per-sample predictive standard deviation of Bayesian Ridge clocks. Default NULL keeps it for every Bayesian ridge clock, as a <column>_sd column. Pass these to the se_columns argument of tage_compare_groups for the Bayesian ridge statistics.

age_units

Units of chronological-age predictions: "auto" (default; months for rodents, years for primates), "months" or "years".

normalized_age

Scale of normalized-age clocks: "fraction" of the expected maximum lifespan (default) or "percent" (x100, as in the paper).

Value

Data frame with predictions for all strata combined (the split_by column is part of the sample metadata).