wrapper_report_LO: wrapper report LO

In CharlesJB/rnaseq: Wrapper Functions for RNA-Seq Post-Processing

wrapper report LO

Description

From metadata and txi, this wrapper parse the metadata and perform all the PCA and volcano (DE). It produces a Rmd file which can be rendered.

Usage

wrapper_report_LO(
  metadata,
  txi,
  outdir,
  pca_subset,
  pca_batch_metadata,
  do_pca = TRUE,
  do_DE = TRUE,
  produce_rmd_report = TRUE,
  render_repport = TRUE,
  extra_count_matrix = NULL,
  volcano_split = NULL,
  volcano_facet_x = NULL,
  volcano_facet_y = NULL,
  custom_parsed_metadata = NULL
)

Arguments

metadata	(data.frame) sample sheet with at least the columns: ID, Compound, Time, Vehicule, Dose, Cell
txi	(list) txi object
pca_subset	(character) column of metadata, filter for automated PCA (ex.: Cell type)
pca_batch_metadata	(character) extra columns for pca coloring (biological or batch effects)
do_pca	(logical) do PCA and included the results in report (default = TRUE)
do_DE	(logical) do DE and included the results in report (default = TRUE)
render_repport	(logical) render Rmd report
custom_parsed_metadata	(list of data.frame) when automatic parsing can be problematic
report_title	(character), title in the report

Value

a list containing pca, volcano and report

CharlesJB/rnaseq documentation built on Oct. 17, 2023, 5:37 p.m.