Data Analysis Modules: panoply_clumps_ptm_diffexp

panoply_clumps_ptm_diffexp

Description

This module performs differential-expression analysis across all features from the provided PTM datasets, for each of the annotations provided in groupsFile. It produces .tsv file(s) for each annotation-column, which can be used as input to Clumps-PTM analysis.

Input

Required inputs:

• pSTY_gct: (.gct file) phosphoproteome data matrix

• acK_gct: (.gct file) acetylome data matrix

• ubK_gct: (.gct file) ubiquitylome data matrix

• groupsFile: (.csv file) annotation file, subsetted to annotations of interest for this analysis

• output_prefix: (String, default="results") prefix used to name the output tar file

• yaml_file: (.yaml file) master-parameters.yaml

Optional inputs:

• sample_id_col: (String, default="Sample.ID") column in groupsFile with sample identifiers.
• fdr_cutoff: (Float, default=NULL) FDR threshold for significant features. Set to NULL to keep all features regardless of significance.
• min_samples: (Int) minimum number of samples an annotation-subgroup can have before it is dropped from analysis (5 recommended, 3 absolute minimum)
• max_annot_levels: (Int) maximum number of levels an annotation can have and be considered discrete

Output

• diff_exp_files: .tsv file(s) containing results of differential-expression analysis, for each of the annotation-columns in groupsFile.
• log_file: (.csv file) Log file which lists every annotation tested, along with whether analysis was valid and had results.