identify_conditions: Identify conditions (background, time of stimulation,...

View source: R/Main_functions.R

identify_conditionsR Documentation

Identify conditions (background, time of stimulation, biological and technical replicates) from column names

Description

Identify conditions (background, time of stimulation, biological and technical replicates) from column names

Usage

identify_conditions(
  df,
  Column_intensity_pattern = "^Intensity.",
  split = "_",
  bait_pos = 0,
  bckg_pos = 1,
  bio_pos = 3,
  time_pos = 2,
  tech_pos = 4
)

Arguments

df

A dataframe containing protein intensities. By default, protein intensity column names start by "Intensity." (use parameter Column_intensity_pattern to change)

Column_intensity_pattern

Pattern (regular exrpression) used to identfy df's columns containing protein intensity values

split

Character used to split column names into substrings

bait_pos

Position of the bait name in splitted column names

bckg_pos

Position of the sample background in splitted column names

bio_pos

Position of the sample biological replicate in splitted column names

time_pos

Position of the sample experimental condition in splitted column names

tech_pos

Position of the sample technical replicate in splitted column names

Value

a data frame describing experimental samples in terms of background, biological and technical replicates, and experimental conditions

Examples

#load data :
data("proteinGroups_Cbl")
# You can identify columns and their description separately using `identify_conditions()`
cond <- identify_conditions(proteinGroups_Cbl)
print.data.frame(cond)
# and use it as parameters for function InteRact()
res <- InteRact(proteinGroups_Cbl, bait_gene_name = "Cbl", condition = cond)

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