preprocess_data: Preprocessing of raw data

In VoisinneG/InteRact: Analysis of affinity purification/tandem MS data

Preprocessing of raw data

Description

Preprocessing of raw data

Usage

preprocess_data(
  df,
  Column_gene_name = "Gene.names",
  Column_score = "Score",
  Column_ID = "Protein.IDs",
  Column_Npep = NULL,
  Column_intensity_pattern = "^Intensity.",
  bait_gene_name,
  condition = NULL,
  bckg_bait = bait_gene_name,
  bckg_ctrl = "WT",
  log = TRUE,
  filter_time = NULL,
  filter_bio = NULL,
  filter_tech = NULL,
  min_score = 0,
  filter_gene_name = TRUE,
  ...
)

Arguments

df	Data.frame with protein intensities
Column_gene_name	Column with gene names
Column_score	Column with protein identification score
Column_ID	Column with protein IDs
Column_Npep	Column with number of theoretically observable peptides per protein
Column_intensity_pattern	Pattern (regular exrpression) used to identfy df's columns containing protein intensity values
bait_gene_name	The gene name of the bait
condition	data.frame with columns "column", bckg", "bio", "time" and "tech" indicating for each intensity column ("sample") its corresponding background ("bckg"), biologicla replicate ("bio), experimental condition ("tine) and technical replicate ("tech).
bckg_bait	Name of the bait background as found in condition$bckg (see below)
bckg_ctrl	Name of the control background as found in condition$bckg (see below)
log	logical, use geometric mean to average technical replicates
filter_time	vector of experimental conditions to exclude from analysis
filter_bio	vector of biological replicates to exclude from analysis
filter_tech	vector of technical replicates to exclude from analysis
min_score	threshold on identification score
filter_gene_name	logical, filter out proteins withy empty gene name
...	Additional parameters passed to function identify_conditions

Examples

#load data :
data("proteinGroups_Cbl")
df <- preprocess_data(proteinGroups_Cbl, bait_gene_name = "Cbl")

VoisinneG/InteRact documentation built on May 17, 2022, 11:40 p.m.