fixCalibration {PTXQC}

Detect (and fix) MaxQuant mass recalibration columns, since they sometimes report wrong values.

Description

Returns a list of items for both diagnostics and possibly a fixed evidence data.frame. Also two strings with messages are returned, which can serve as user message for pre and post calibration status.

Usage

fixCalibration(
  df_evd,
  df_idrate = NULL,
  tolerance_sd_PCoutOfCal = 2,
  low_id_rate = 1
)

Arguments

df_evd

Evidence data.frame with columns ()

df_idrate

Data.frame from summary.txt, giving ID rates for each raw file (cols: "ms.ms.identified....", "fc.raw.file"). Can also be NULL.

tolerance_sd_PCoutOfCal

Maximal standard deviation allowed before considered 'failed'

low_id_rate

Minimum ID rate in Percent before a Raw file is considered 'failed'

Value

list of data (stats, affected_raw_files, df_evd, recal_message, recal_message_post)