Computes, from the GTEx v8 median transcript TPM of one tissue (frozen
dataset gtex_transcript_tpm, frozen_data) and the productivity calls
of x, the reference state of every gene in healthy tissue: its
productive fraction, its dominant isoform and the dominant isoform's
productivity. productive_fraction() accepts the result (or a tissue
name) as reference and reports the difference between the samples and
the tissue baseline, which separates a disease-specific loss of
productive isoforms from a tissue's normal state.
Transcript identifiers are matched without version; GTEx v8 uses GENCODE v26, so transcripts annotated later have no reference value.
Usage
gtex_reference(self, tissue, gtex = NULL, include_altered = TRUE, ...)
gtex_tissues(gtex = NULL)Arguments
- self
- tissue
GTEx tissue name (
SMTSD, for example"Whole Blood","Brain - Cortex"); seegtex_tissues().- gtex
Data frame or Parquet path of the GTEx table;
NULLfetches the frozen dataset.- include_altered
Logical, count
altered_productiveisoforms as productive (defaultTRUE).- ...
Passed on to methods.
Value
A tibble with one row per gene of x: reference_tissue,
reference_gene_tpm, reference_productive_fraction,
reference_dominant_transcript_id, reference_dominant_productivity,
n_reference_transcripts.
Examples
if (FALSE) { # \dontrun{
iso <- example_isoformic()
ref <- gtex_reference(iso, tissue = "Whole Blood")
productive_fraction(iso, group = "condition", reference = ref)
} # }