Data Analysis Modules: panoply_omicsev

panoply_omicsev

Description

A tool for large scale omics data tables evaluation. Find full OmicsEV documentation here.

Inputs

Required Inputs

General mandatory inputs:

• STANDALONE (String): Either "true" or "false". Determines whether OmicsEV should run as part of panoply_main pipeline with inputs from panoply_harmonize, or if OmicsEV should run independently with .gct inputs. Preference is to run with STANDALONE == "false" if possible.
• yaml_file (File): Parameters yaml file from PANOPLY setup. Must contain gene.id.col, groups information, an defaults for OmicsEV parameters.
• label (String): Label for this data set (e.g. "BRCA.proteome"). HTML report will include this label in the file name.

Mandatory inputs if STANDALONE = "false":

• panoply_harmonize_tar_file (File): Tar output from panoply_harmonize module.
• ome_type (String): The PANOPLY omics type of the input (e.g. "proteome").

Mandatory inputs if STANDALONE = "true":

• data_files (Array[File]): Array of .gct files to be used for OmicsEV. These are typically all the same -ome from the same samples with some variation in how abundance values were calculated. For example, multiple proteome files generated using different batch correction methods. Array[File] format is ["/path/to/file-1.gct","/path/to/file-2.gct","/path/to/file-3.gct"]. Make sure there is no space between each file, just a single comma. A single data file input is acceptable (e.g. ["/path/to/file-1.gct"]).
• sample_anno_file (File): A .csv file with sample annotations. File must include same samples as are in data_files. This file must have columns labeled with class_column_name and batch_column_name (or their PANOPLY defaults, see below).

Optional Inputs

General optional inputs:

• class_column_name (String): Column in sample annotation file that contains class information. This should be a categorical annotation (e.g. sex, cancer type, etc.) to assess differences between phenotypes. The default in the PANOPLY yaml file is "Type". If class_column_name is not found in the sample annotation file, the default behavior is to include all samples in an artificial class called "Default".
• batch_column_name (String): Column in sample annotation file that contains batch information. This is used to assess batch effects. Must be integer values with no NA's. If STANDALONE = true, this can also be a column in the column-description of each .gct file in data_files. The default in the PANOPLY yaml file is "Experiment", which is found in outputs from SpectrumMill. If batch_column_name is not found in the sample annotation file, the default behavior is to include all samples in an artificial batch (batch = 1).
• data_log_transformed (Boolean): Indicates whether the protein-level data has been log transformed.
• rna_log_transformed (Boolean): Indicates whether the rna data has been log transformed.
• do_function_prediction (Boolean): Whether or not to perform gene function prediction analysis. If this is not necessary, it is suggested to turn this off. Gene function prediction takes a considerable amount of time. Default in PANOPLY yaml file is false.

Optional inputs if STANDALONE = true:

• rna_file (File): A .gct file of RNAseq data. Used only for RNA-protein correlation at the end of OmicsEV.

Outputs

• report (File): An HTML report of OmicsEV evaluation metrics for each dataset.
• outputs (File): A tarball with the full OmicsEV outputs, including intermediary tables and figures.