Class representing an expression dataset at transcript-level

Extension of expression dataset at transcript-level

Super class

nexodiff::ExprData -> ExprDataTranscript

Methods

Public methods

• ExprDataTranscript$new()

• ExprDataTranscript$clone()

Inherited methods

• nexodiff::ExprData$clean_id_versions()
• nexodiff::ExprData$compute_and_set_inter_norm_fact()
• nexodiff::ExprData$compute_and_set_intra_norm_fact()
• nexodiff::ExprData$compute_norm()
• nexodiff::ExprData$compute_norm_fact()
• nexodiff::ExprData$extract_pairwise_data_with_design()
• nexodiff::ExprData$filter_and_get_len()
• nexodiff::ExprData$filter_and_get_raw()
• nexodiff::ExprData$filter_and_set_selected_ids()
• nexodiff::ExprData$get_annotation()
• nexodiff::ExprData$get_design()
• nexodiff::ExprData$get_inter_norm_fact()
• nexodiff::ExprData$get_inter_norm_fact_opts()
• nexodiff::ExprData$get_intra_norm_fact()
• nexodiff::ExprData$get_intra_norm_fact_method()
• nexodiff::ExprData$get_len()
• nexodiff::ExprData$get_main_etag()
• nexodiff::ExprData$get_raw()
• nexodiff::ExprData$is_at_gene_level()
• nexodiff::ExprData$is_with_fixed_length()
• nexodiff::ExprData$plot_corr()
• nexodiff::ExprData$plot_dist_per_sample()
• nexodiff::ExprData$plot_etags_summary()
• nexodiff::ExprData$plot_hclust()
• nexodiff::ExprData$plot_prcomp()
• nexodiff::ExprData$reset()
• nexodiff::ExprData$show_etags_summary()

---

Method new()

Initialize ExprDataTranscript object

Usage

ExprDataTranscript$new(
  design,
  annotation,
  with_fixed_length = FALSE,
  log_level = "WARN",
  suffix_pattern = "\\.\\d+$"
)

Arguments

design

A pairwise design object PairwiseDesign

annotation

An annotation object Annotation

with_fixed_length

A boolean indicating whether the NGS library is of a fixed length like 3 prime or not

log_level

Level of logging (see logging package). Default = WARN

suffix_pattern

See clean_txid_versions method Default = txid

Returns

A new ExprDataTranscript object.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

ExprDataTranscript$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.