createYaml {PTXQC}

Creates a yaml file storing the parameters that are used for creating the PTXQC report and returns these parameters as well as a list of available qc-Metrics objects.

Description

Valid parameters are: param_useMQPAR, add_fs_col, id_rate_bad, id_rate_great , pg_ratioLabIncThresh , param_PG_intThresh, param_EV_protThresh , param_EV_intThresh, param_EV_pepThresh , yaml_contaminants, param_EV_MatchingTolerance, param_evd_mbr , param_EV_PrecursorTolPPM, param_EV_PrecursorOutOfCalSD , param_EV_PrecursorTolPPMmainSearch, param_MSMSScans_ionInjThresh, param_OutputFormats and param_PageNumbers

Please provide them as a list() of this format: list$parameter_name

Usage

createYaml(
  yc,
  param = list(),
  DEBUG_PTXQC = FALSE,
  txt_files = NULL,
  metrics = NULL
)

Arguments

yc

A yaml class object created by YAMLClass$new()

param

list of parameters sorted by names; if empty, will be populated with defaults

DEBUG_PTXQC

print some debugging information; default FALSE

txt_files

list of paths to MaxQuant files; if NULL, it is assumed that the parameters are for mzTab-mode

metrics

list of metric names that should be plotted; if NULL, will be populated with defaults

Value

list of parameters used for creating the report and list of qc-Metrics objects