artMS configuration for the available PH dataset

The configuration file with default options to run the available PH dataset with `artmsQuantification()``

artms_data_ph_config

Format

The configuration (yaml) file contains the following sections:

files

• evidence : Empty. To test an example, run artms_data_ph_config$files$evidence <- artms_data_ph_evidence

• keys : Empty To test an example datasets run artms_data_ph_config$files$keys <- artms_data_ph_keys

• contrasts : Empty. To test the example datasets, run artms_data_ph_config$files$contrasts <- artms_data_ph_contrast

• summary :

• output : "results.txt"

qc

• basic: 0

• extended: 0

• extendedSummary: 0

data

• enabled : 1

• silac:

  • enabled : 0

• filters:

  • enabled : 1

• contaminants : 1

• protein_groups : remove

• modifications : PH

• sample_plots : 1

msstats

• enabled : 1

• msstats_input : # blank if not previous msstats input file is available

• profilePlots : none # before, after, before-after, none

• normalization_method : equalizeMedians

• normalization_reference : #should be a value in the Protein column

• summaryMethod : TMP

• censoredInt : NA

• cutoffCensored : minFeature

• MBimpute : 1

• feature_subset: all

output_extras

• output_extras :

  • enabled : 1

• annotate :

  • enabled: 1

• species : HUMAN

• plots:

  • volcano: 1

  • heatmap: 1

  • LFC : -1 1

  • FDR : 0.05

  • heatmap_cluster_cols : 0

  • heatmap_display : log2FC