removeTrend: Removes trend from a batch of DIA-NN experiment

In alzel/proteomicsQC: A set of Routines to plot and analyse DIA-NN reports

Removes trend from a batch of DIA-NN experiment

Description

Removes trend from a batch of DIA-NN experiment

Usage

removeTrend(
  report,
  metadata,
  QC_regex = "MSQC",
  fit_model = "loess",
  feature_var = "Precursor.Id",
  feature_value = "Precursor.Quantity"
)

Arguments

report	DIA-NN report file
metadata	metadata experiment description to arrange by run_order output from create_metadata
QC_regex	regexp to extract QC values for fitting model
fit_model	model to fit, one of lm, loess, rq (robust regression using medians)
feature_value	feature value to remove trend from, default: "Precursor.Quantity"
feature_var	feature variable, default: "Precursor.Id"

Value

returns tbl with corrected feature values from feature_var

Examples

metadata <- create_metadata(diann_report)
diann_report magrittr::`%>%`()
   dplyr::filter(!grepl(pattern = "blank", x="File.Name", ignore.case = T)) magrittr::`%>%`()
   removeTrend(metadata = metadata, QC_regex = "MSQC", fit_model = "lm",
   feature_var = "Precursor.Id" , feature_value = "Precursor.Quantity" ) -> Precursor.Id_corrected

alzel/proteomicsQC documentation built on Aug. 11, 2022, 5:58 p.m.