View source: R/Main_functions.R
identify_conditions | R Documentation |
Identify conditions (background, time of stimulation, biological and technical replicates) from column names
identify_conditions( df, Column_intensity_pattern = "^Intensity.", split = "_", bait_pos = 0, bckg_pos = 1, bio_pos = 3, time_pos = 2, tech_pos = 4 )
df |
A dataframe containing protein intensities. By default, protein intensity column names start by "Intensity."
(use parameter |
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 |
a data frame describing experimental samples in terms of background, biological and technical replicates, and experimental conditions
#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)
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