Extract information from FragPipe logs

Read FragPipe config/log files and extract information about the run.

readFragPipeInfo(fragpipeDir)

Arguments

fragpipeDir

Character scalar, the path to a FragPipe output directory. Should contain files <fragpipeDir>/fragpipe_*.config (or <fragpipeDir>/fragpipe.workflow) and <fragpipeDir>/log_*.txt (if not, the corresponding fields will be empty in the output).

Value

A list with extracted information about the FragPipe run.

Author

Charlotte Soneson, Jan Seebacher

Examples

readFragPipeInfo(system.file("extdata", "fp_example",
                             package = "einprot"))
#> $`FragPipe version`
#> [1] "19.1"
#> 
#> $`FragPipe parameter file`
#> [1] "/Users/runner/work/_temp/Library/einprot/extdata/fp_example/fragpipe.workflow"
#> 
#> $`FragPipe log file`
#> [1] "/Users/runner/work/_temp/Library/einprot/extdata/fp_example/log_2023-04-12_20-12-46.txt"
#> 
#> $`Search engine`
#> [1] "MSFragger-3.7"
#> 
#> $`Raw file location`
#> [1] "D:/Data/FUSION"
#> 
#> $`Raw files`
#> [1] "F_160817_AdnpFB_IP06.raw, F_160817_AdnpFB_IP05.raw, F_160817_RBC_ctrl_IP02.raw, F_160817_AdnpFB_IP04.raw, F_160817_RBC_ctrl_IP01.raw, F_160817_Chd4BF_IP09.raw, F_160817_Chd4BF_IP07.raw, F_160817_Chd4BF_IP08.raw, F_160817_RBC_ctrl_IP03.raw"
#> 
#> $`Sample names`
#> [1] "Adnp_IP04, Adnp_IP05, Adnp_IP06, Chd4BF_IP07, Chd4BF_IP08, Chd4BF_IP09, RBC_ctrl_IP01, RBC_ctrl_IP02, RBC_ctrl_IP03"
#> 
#> $Databases
#> [1] "D/://Data//FASTA//2023-04-12-decoys-contam_MOUSE__190410.fasta.fas"
#> 
#> $`Peptides (ranges)`
#> [1] "length: 7-50 AA; mass: 500-5000 Da"
#> 
#> $`Mass error tolerances`
#> [1] "precursor:-20-20 [ppm]; fragment:0.7 [Da] (after optimization:200 PPM)"
#> 
#> $`Quantification settings (LFQ)`
#> [1] "IonQuant: TRUE, Calculate MaxLFQ intensity: TRUE, Normalization: TRUE, match-between runs (MBR): FALSE, min. ions: 2, Top N ions: 3"
#> 
#> $Enzymes
#> [1] "stricttrypsin[KR, C-terminal, 2 missed cleavages]"
#> 
#> $`Variable modifications`
#> [1] "M(15.9949), N-term(42.0106)"
#> 
#> $`Fixed modifications`
#> [1] "C(57.0215)"
#> 
#> $`Database decoy tag`
#> [1] "rev_"
#>