validate_inputs: Call the various read/ validate methods for input data...

In pinin4fjords/shinyngs: Shiny apps for NGS data

Call the various read/ validate methods for input data surrounding an experiment

Description

Call the various read/ validate methods for input data surrounding an experiment

Usage

validate_inputs(
  samples_metadata,
  assay_files,
  contrasts_file = NULL,
  features_metadata = NULL,
  sample_id_col = "sample",
  assay_names = NULL,
  differential_results = NULL,
  feature_id_col = "gene_id",
  pval_column = "pval_column",
  qval_column = "qval_column",
  fc_column = "log2FoldChange",
  unlog_foldchanges = FALSE
)

Arguments

samples_metadata	Sample metadata data frame
assay_files	List of assay matrices
contrasts_file	Contrasts definition file
features_metadata	Feature metadata data frame
sample_id_col	Column of sample metadata used for identifiers
assay_names	Optional comma-separated list of assay names
differential_results	Optional list of differential stats files
feature_id_col	Column of feature metadata used for identifiers
pval_column	P value column if differential stats files specified
qval_column	Q value column if differential stats files specified
fc_column	Fold change column if differential stats files specified
unlog_foldchanges	Boolean- should fold changes in stats files be unlogged?

Value

output A named list with feature/ observation components

pinin4fjords/shinyngs documentation built on Jan. 18, 2025, 7:09 p.m.