prepare_annotations_for_fungiexpres_data_matrix: Prepare SRA sample annotations required for FungiExpresZ.

In cparsania/FungiExpresZ: FungiExpresZ: Fungal gene expression data analysis and visualizations

Prepare SRA sample annotations required for FungiExpresZ.

Description

Prepare SRA sample annotations required for FungiExpresZ.

Usage

prepare_annotations_for_fungiexpres_data_matrix(
  data_matrix,
  fungiexpresz_species,
  fungiexpresz_ref_annotation,
  fungal_sra_run_info_object_path,
  path_sra_db_sqlite_file
)

Arguments

data_matrix	a FPKM matrix for which SRA annotations to be obtained. Column names of will be considered as SRA id.
fungiexpresz_species	a character string denoting a species name for the 'data_matrix'. Species must present in the FungiExpresZ GO annotations.
fungiexpresz_ref_annotation	a character denoting a reference annotation for the species. Reference annotation must present in the FungiExpresZ GO annotations.
fungal_sra_run_info_object_path	a character string denoting path to the 'fungal_sra_run_info_table.rds' object.
path_sra_db_sqlite_file	a character string denoting path to the 'SRAmetadb.sqlite' object.

Value

a tibble of SRA annotation which can be append to existing 'sample_info' object of FungiExpresZ.

cparsania/FungiExpresZ documentation built on March 15, 2024, 5:48 p.m.