R/Main_functions.R
identify_conditions.RdIdentify conditions (background, time of stimulation, biological and technical replicates) from column names
identify_conditions(df, Column_intensity_pattern = "^Intensity.", split = "_", 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 |
| 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)#> column bckg time bio tech #> 1 Intensity.Cbl_0_Ech1_R1 Cbl 0 Ech1 R1 #> 2 Intensity.Cbl_0_Ech1_R2 Cbl 0 Ech1 R2 #> 3 Intensity.Cbl_0_Ech1_R3 Cbl 0 Ech1 R3 #> 4 Intensity.Cbl_0_Ech2_R1 Cbl 0 Ech2 R1 #> 5 Intensity.Cbl_0_Ech2_R2 Cbl 0 Ech2 R2 #> 6 Intensity.Cbl_0_Ech2_R3 Cbl 0 Ech2 R3 #> 7 Intensity.Cbl_0_Ech3_R1 Cbl 0 Ech3 R1 #> 8 Intensity.Cbl_0_Ech3_R2 Cbl 0 Ech3 R2 #> 9 Intensity.Cbl_0_Ech3_R3 Cbl 0 Ech3 R3 #> 10 Intensity.Cbl_030_Ech1_R1 Cbl 030 Ech1 R1 #> 11 Intensity.Cbl_030_Ech1_R2 Cbl 030 Ech1 R2 #> 12 Intensity.Cbl_030_Ech1_R3 Cbl 030 Ech1 R3 #> 13 Intensity.Cbl_030_Ech2_R1 Cbl 030 Ech2 R1 #> 14 Intensity.Cbl_030_Ech2_R2 Cbl 030 Ech2 R2 #> 15 Intensity.Cbl_030_Ech2_R3 Cbl 030 Ech2 R3 #> 16 Intensity.Cbl_030_Ech3_R1 Cbl 030 Ech3 R1 #> 17 Intensity.Cbl_030_Ech3_R2 Cbl 030 Ech3 R2 #> 18 Intensity.Cbl_030_Ech3_R3 Cbl 030 Ech3 R3 #> 19 Intensity.Cbl_120_Ech1_R1 Cbl 120 Ech1 R1 #> 20 Intensity.Cbl_120_Ech1_R2 Cbl 120 Ech1 R2 #> 21 Intensity.Cbl_120_Ech1_R3 Cbl 120 Ech1 R3 #> 22 Intensity.Cbl_120_Ech2_R1 Cbl 120 Ech2 R1 #> 23 Intensity.Cbl_120_Ech2_R2 Cbl 120 Ech2 R2 #> 24 Intensity.Cbl_120_Ech2_R3 Cbl 120 Ech2 R3 #> 25 Intensity.Cbl_120_Ech3_R1 Cbl 120 Ech3 R1 #> 26 Intensity.Cbl_120_Ech3_R2 Cbl 120 Ech3 R2 #> 27 Intensity.Cbl_120_Ech3_R3 Cbl 120 Ech3 R3 #> 28 Intensity.Cbl_300_Ech1_R1 Cbl 300 Ech1 R1 #> 29 Intensity.Cbl_300_Ech1_R2 Cbl 300 Ech1 R2 #> 30 Intensity.Cbl_300_Ech1_R3 Cbl 300 Ech1 R3 #> 31 Intensity.Cbl_300_Ech2_R1 Cbl 300 Ech2 R1 #> 32 Intensity.Cbl_300_Ech2_R2 Cbl 300 Ech2 R2 #> 33 Intensity.Cbl_300_Ech2_R3 Cbl 300 Ech2 R3 #> 34 Intensity.Cbl_300_Ech3_R1 Cbl 300 Ech3 R1 #> 35 Intensity.Cbl_300_Ech3_R2 Cbl 300 Ech3 R2 #> 36 Intensity.Cbl_300_Ech3_R3 Cbl 300 Ech3 R3 #> 37 Intensity.Cbl_600_Ech1_R1 Cbl 600 Ech1 R1 #> 38 Intensity.Cbl_600_Ech1_R2 Cbl 600 Ech1 R2 #> 39 Intensity.Cbl_600_Ech1_R3 Cbl 600 Ech1 R3 #> 40 Intensity.Cbl_600_Ech2_R1 Cbl 600 Ech2 R1 #> 41 Intensity.Cbl_600_Ech2_R2 Cbl 600 Ech2 R2 #> 42 Intensity.Cbl_600_Ech2_R3 Cbl 600 Ech2 R3 #> 43 Intensity.Cbl_600_Ech3_R1 Cbl 600 Ech3 R1 #> 44 Intensity.Cbl_600_Ech3_R2 Cbl 600 Ech3 R2 #> 45 Intensity.Cbl_600_Ech3_R3 Cbl 600 Ech3 R3 #> 46 Intensity.WT_0_Ech1_R1 WT 0 Ech1 R1 #> 47 Intensity.WT_0_Ech1_R2 WT 0 Ech1 R2 #> 48 Intensity.WT_0_Ech1_R3 WT 0 Ech1 R3 #> 49 Intensity.WT_0_Ech2_R1 WT 0 Ech2 R1 #> 50 Intensity.WT_0_Ech2_R2 WT 0 Ech2 R2 #> 51 Intensity.WT_0_Ech2_R3 WT 0 Ech2 R3 #> 52 Intensity.WT_0_Ech3_R1 WT 0 Ech3 R1 #> 53 Intensity.WT_0_Ech3_R2 WT 0 Ech3 R2 #> 54 Intensity.WT_0_Ech3_R3 WT 0 Ech3 R3 #> 55 Intensity.WT_030_Ech1_R1 WT 030 Ech1 R1 #> 56 Intensity.WT_030_Ech1_R2 WT 030 Ech1 R2 #> 57 Intensity.WT_030_Ech1_R3 WT 030 Ech1 R3 #> 58 Intensity.WT_030_Ech2_R1 WT 030 Ech2 R1 #> 59 Intensity.WT_030_Ech2_R2 WT 030 Ech2 R2 #> 60 Intensity.WT_030_Ech2_R3 WT 030 Ech2 R3 #> 61 Intensity.WT_030_Ech3_R1 WT 030 Ech3 R1 #> 62 Intensity.WT_030_Ech3_R2 WT 030 Ech3 R2 #> 63 Intensity.WT_030_Ech3_R3 WT 030 Ech3 R3 #> 64 Intensity.WT_120_Ech1_R1 WT 120 Ech1 R1 #> 65 Intensity.WT_120_Ech1_R2 WT 120 Ech1 R2 #> 66 Intensity.WT_120_Ech1_R3 WT 120 Ech1 R3 #> 67 Intensity.WT_120_Ech2_R1 WT 120 Ech2 R1 #> 68 Intensity.WT_120_Ech2_R2 WT 120 Ech2 R2 #> 69 Intensity.WT_120_Ech2_R3 WT 120 Ech2 R3 #> 70 Intensity.WT_120_Ech3_R1 WT 120 Ech3 R1 #> 71 Intensity.WT_120_Ech3_R2 WT 120 Ech3 R2 #> 72 Intensity.WT_120_Ech3_R3 WT 120 Ech3 R3 #> 73 Intensity.WT_300_Ech1_R1 WT 300 Ech1 R1 #> 74 Intensity.WT_300_Ech1_R2 WT 300 Ech1 R2 #> 75 Intensity.WT_300_Ech1_R3 WT 300 Ech1 R3 #> 76 Intensity.WT_300_Ech2_R1 WT 300 Ech2 R1 #> 77 Intensity.WT_300_Ech2_R2 WT 300 Ech2 R2 #> 78 Intensity.WT_300_Ech2_R3 WT 300 Ech2 R3 #> 79 Intensity.WT_300_Ech3_R1 WT 300 Ech3 R1 #> 80 Intensity.WT_300_Ech3_R2 WT 300 Ech3 R2 #> 81 Intensity.WT_300_Ech3_R3 WT 300 Ech3 R3 #> 82 Intensity.WT_600_Ech1_R1 WT 600 Ech1 R1 #> 83 Intensity.WT_600_Ech1_R2 WT 600 Ech1 R2 #> 84 Intensity.WT_600_Ech1_R3 WT 600 Ech1 R3 #> 85 Intensity.WT_600_Ech2_R1 WT 600 Ech2 R1 #> 86 Intensity.WT_600_Ech2_R2 WT 600 Ech2 R2 #> 87 Intensity.WT_600_Ech2_R3 WT 600 Ech2 R3 #> 88 Intensity.WT_600_Ech3_R1 WT 600 Ech3 R1 #> 89 Intensity.WT_600_Ech3_R2 WT 600 Ech3 R2 #> 90 Intensity.WT_600_Ech3_R3 WT 600 Ech3 R3# and use it as parameters for function InteRact() res <- InteRact(proteinGroups_Cbl, bait_gene_name = "Cbl", condition = cond)#> Warning: Column 'Score' not available : Data NOT Filtered based on portein identification score#> Contaminant proteins discarded #> Proteins with no gene name available discarded #> Number of theoretically observable peptides unavailable : used MW instead #> Merge protein groups associated to the same gene name (sum of intensities) #> Rescale median intensity across conditions #> Replace missing values and perform interactome analysis for 1 replicates #> Nrep=1 #> Averaging 1 interactomes#> Warning: NaNs produced#> Warning: NaNs produced#> Warning: NaNs produced#> Warning: NaNs produced#> Warning: NaNs produced#> Warning: NaNs produced#> Warning: NaNs produced#> Warning: NaNs produced#> Warning: NaNs produced#> Warning: NaNs produced#> Warning: NaNs produced#> Warning: NaNs produced#> Warning: NaNs produced#> Warning: NaNs produced#> Warning: NaNs produced#> Warning: NaNs produced#> Warning: NaNs produced#> Warning: NaNs produced#> Warning: NaNs produced#> Warning: NaNs produced