getColumnNames.RdUtility function to retrieve column names from quantification text file.
getColumnNames(inFile, ...)Path to a tab-delimited input text file (e.g. MaxQuant
peptideGroups.txt or ProteomeDiscoverer Proteins.txt).
Additional arguments passed on to utils::read.delim().
A character vector with column names (converted to valid names) for the input file.
colnm <- getColumnNames(system.file("extdata", "mq_example",
"1356_proteinGroups.txt",
package = "einprot"))
colnm
#> [1] "Protein.IDs"
#> [2] "Majority.protein.IDs"
#> [3] "Peptide.counts..all."
#> [4] "Peptide.counts..razor.unique."
#> [5] "Peptide.counts..unique."
#> [6] "Protein.names"
#> [7] "Gene.names"
#> [8] "Fasta.headers"
#> [9] "Number.of.proteins"
#> [10] "Peptides"
#> [11] "Razor...unique.peptides"
#> [12] "Unique.peptides"
#> [13] "Peptides.Adnp_IP04"
#> [14] "Peptides.Adnp_IP05"
#> [15] "Peptides.Adnp_IP06"
#> [16] "Peptides.Chd4BF_IP07"
#> [17] "Peptides.Chd4BF_IP08"
#> [18] "Peptides.Chd4BF_IP09"
#> [19] "Peptides.RBC_ctrl_IP01"
#> [20] "Peptides.RBC_ctrl_IP02"
#> [21] "Peptides.RBC_ctrl_IP03"
#> [22] "Razor...unique.peptides.Adnp_IP04"
#> [23] "Razor...unique.peptides.Adnp_IP05"
#> [24] "Razor...unique.peptides.Adnp_IP06"
#> [25] "Razor...unique.peptides.Chd4BF_IP07"
#> [26] "Razor...unique.peptides.Chd4BF_IP08"
#> [27] "Razor...unique.peptides.Chd4BF_IP09"
#> [28] "Razor...unique.peptides.RBC_ctrl_IP01"
#> [29] "Razor...unique.peptides.RBC_ctrl_IP02"
#> [30] "Razor...unique.peptides.RBC_ctrl_IP03"
#> [31] "Unique.peptides.Adnp_IP04"
#> [32] "Unique.peptides.Adnp_IP05"
#> [33] "Unique.peptides.Adnp_IP06"
#> [34] "Unique.peptides.Chd4BF_IP07"
#> [35] "Unique.peptides.Chd4BF_IP08"
#> [36] "Unique.peptides.Chd4BF_IP09"
#> [37] "Unique.peptides.RBC_ctrl_IP01"
#> [38] "Unique.peptides.RBC_ctrl_IP02"
#> [39] "Unique.peptides.RBC_ctrl_IP03"
#> [40] "Sequence.coverage...."
#> [41] "Unique...razor.sequence.coverage...."
#> [42] "Unique.sequence.coverage...."
#> [43] "Mol..weight..kDa."
#> [44] "Sequence.length"
#> [45] "Sequence.lengths"
#> [46] "Q.value"
#> [47] "Score"
#> [48] "Identification.type.Adnp_IP04"
#> [49] "Identification.type.Adnp_IP05"
#> [50] "Identification.type.Adnp_IP06"
#> [51] "Identification.type.Chd4BF_IP07"
#> [52] "Identification.type.Chd4BF_IP08"
#> [53] "Identification.type.Chd4BF_IP09"
#> [54] "Identification.type.RBC_ctrl_IP01"
#> [55] "Identification.type.RBC_ctrl_IP02"
#> [56] "Identification.type.RBC_ctrl_IP03"
#> [57] "Sequence.coverage.Adnp_IP04...."
#> [58] "Sequence.coverage.Adnp_IP05...."
#> [59] "Sequence.coverage.Adnp_IP06...."
#> [60] "Sequence.coverage.Chd4BF_IP07...."
#> [61] "Sequence.coverage.Chd4BF_IP08...."
#> [62] "Sequence.coverage.Chd4BF_IP09...."
#> [63] "Sequence.coverage.RBC_ctrl_IP01...."
#> [64] "Sequence.coverage.RBC_ctrl_IP02...."
#> [65] "Sequence.coverage.RBC_ctrl_IP03...."
#> [66] "Intensity"
#> [67] "Intensity.Adnp_IP04"
#> [68] "Intensity.Adnp_IP05"
#> [69] "Intensity.Adnp_IP06"
#> [70] "Intensity.Chd4BF_IP07"
#> [71] "Intensity.Chd4BF_IP08"
#> [72] "Intensity.Chd4BF_IP09"
#> [73] "Intensity.RBC_ctrl_IP01"
#> [74] "Intensity.RBC_ctrl_IP02"
#> [75] "Intensity.RBC_ctrl_IP03"
#> [76] "iBAQ"
#> [77] "iBAQ.Adnp_IP04"
#> [78] "iBAQ.Adnp_IP05"
#> [79] "iBAQ.Adnp_IP06"
#> [80] "iBAQ.Chd4BF_IP07"
#> [81] "iBAQ.Chd4BF_IP08"
#> [82] "iBAQ.Chd4BF_IP09"
#> [83] "iBAQ.RBC_ctrl_IP01"
#> [84] "iBAQ.RBC_ctrl_IP02"
#> [85] "iBAQ.RBC_ctrl_IP03"
#> [86] "LFQ.intensity.Adnp_IP04"
#> [87] "LFQ.intensity.Adnp_IP05"
#> [88] "LFQ.intensity.Adnp_IP06"
#> [89] "LFQ.intensity.Chd4BF_IP07"
#> [90] "LFQ.intensity.Chd4BF_IP08"
#> [91] "LFQ.intensity.Chd4BF_IP09"
#> [92] "LFQ.intensity.RBC_ctrl_IP01"
#> [93] "LFQ.intensity.RBC_ctrl_IP02"
#> [94] "LFQ.intensity.RBC_ctrl_IP03"
#> [95] "MS.MS.Count.Adnp_IP04"
#> [96] "MS.MS.Count.Adnp_IP05"
#> [97] "MS.MS.Count.Adnp_IP06"
#> [98] "MS.MS.Count.Chd4BF_IP07"
#> [99] "MS.MS.Count.Chd4BF_IP08"
#> [100] "MS.MS.Count.Chd4BF_IP09"
#> [101] "MS.MS.Count.RBC_ctrl_IP01"
#> [102] "MS.MS.Count.RBC_ctrl_IP02"
#> [103] "MS.MS.Count.RBC_ctrl_IP03"
#> [104] "MS.MS.Count"
#> [105] "Only.identified.by.site"
#> [106] "Reverse"
#> [107] "Potential.contaminant"
#> [108] "id"
#> [109] "Peptide.IDs"
#> [110] "Peptide.is.razor"
#> [111] "Mod..peptide.IDs"
#> [112] "Evidence.IDs"
#> [113] "MS.MS.IDs"
#> [114] "Best.MS.MS"
#> [115] "Oxidation..M..site.IDs"
#> [116] "Oxidation..M..site.positions"