artms_data_ph_config: artMS configuration for the available PH dataset

artms_data_ph_configR Documentation

artMS configuration for the available PH dataset

Description

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

Usage

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


kroganlab/artMS documentation built on July 7, 2023, 5:35 a.m.