A master function combining the entire LDH pipeline into one command to run in R.
Usage
runLDHPipeline(
raw_data,
plate_layout,
platform = "bioplex",
dilution = c(1e+06, 333333.33, 111111.11, 37037.04, 12345.68, 4115.23, 1371.74, 457.25,
152.42, 50.81),
experiment_name = "experiment1",
file_path = NULL
)Arguments
- raw_data
String with the raw data path.
- plate_layout
An ".xlsx" file with sheets labelled plate1, plate2... etc.
- platform
"magpix" or "bioplex". Default: "Bioplex"
- dilution
A list of numbers ranging from S1 to S10. Default: 1000000, 333333.33, 111111.11, 37037.04, 12345.68, 4115.23, 1371.74, 457.25, 152.42, 50.81.
- experiment_name
User-input experiment name. Default: "experiment1".
- file_path
A file path to write the .csv final file. Default: Current working directory.
Value
A data frame containing the MFI and RAU Dilution values for each sample, QC plots for standard curve, bead counts and blanks.
Examples
# \donttest{
# Example input files
your_raw_data <- system.file(
"extdata",
"example_BioPlex_PvLDH_plate1.xlsx",
package = "SeroTrackR"
)
your_plate_layout <- system.file(
"extdata",
"example_platelayout_1.xlsx",
package = "SeroTrackR"
)
# Run full LDH processing pipeline
runLDHPipeline(
raw_data = your_raw_data, # Vector of raw data files
plate_layout = your_plate_layout, # Plate layout file
)
#> PASS: File example_bioplex_pvldh_plate1.xlsx successfully validated.
#> Plate layouts correctly identified!
#> [[1]]
#>
#> [[2]]
#>
#> [[3]]
#> [1] "No repeats necessary."
#>
#> [[4]]
#>
#> [[5]]
#> SampleID Location.2 Location Sample Plate PvLDH-ST_MFI PvLDH-ST_Dilution
#> 1 ABC013 B1 13(1,B1) X13 plate1 54.5 331.46776
#> 2 ABC014 B2 14(1,B2) X14 plate1 28.5 57.56885
#> 3 ABC015 B3 15(1,B3) X15 plate1 33.5 99.51020
#> 4 ABC016 B4 16(1,B4) X16 plate1 32.0 86.11171
#> 5 ABC017 B5 17(1,B5) X17 plate1 33.0 94.97366
#> 6 ABC018 B6 18(1,B6) X18 plate1 30.0 69.29915
#> 7 ABC019 B7 19(1,B7) X19 plate1 15646.5 168506.01492
#> 8 ABC020 B8 20(1,B8) X20 plate1 40.0 163.90899
#> 9 ABC021 B9 21(1,B9) X21 plate1 46.5 235.95779
#> 10 ABC022 B10 22(1,B10) X22 plate1 32.0 86.11171
#> 11 ABC023 B11 23(1,B11) X23 plate1 33.5 99.51020
#> 12 ABC024 B12 24(1,B12) X24 plate1 114.0 1110.14041
#> 13 ABC025 C1 25(1,C1) X25 plate1 29.0 61.38969
#> 14 ABC026 C2 26(1,C2) X26 plate1 48.5 259.24703
#> 15 ABC027 C3 27(1,C3) X27 plate1 41.0 174.57172
#> 16 ABC028 C4 28(1,C4) X28 plate1 52.0 300.99301
#> 17 ABC029 C5 29(1,C5) X29 plate1 29.0 61.38969
#> 18 ABC030 C6 30(1,C6) X30 plate1 28.5 57.56885
#> 19 ABC031 C7 31(1,C7) X31 plate1 38.0 143.13049
#> 20 ABC032 C8 32(1,C8) X32 plate1 27.5 50.20976
#> 21 ABC033 C9 33(1,C9) X33 plate1 40.0 163.90899
#> 22 ABC034 C10 34(1,C10) X34 plate1 23.0 22.40309
#> 23 ABC035 C11 35(1,C11) X35 plate1 32.0 86.11171
#> 24 ABC036 C12 36(1,C12) X36 plate1 26.0 39.92476
#> 25 ABC037 D1 37(1,D1) X37 plate1 32.5 90.50674
#> 26 ABC038 D2 38(1,D2) X38 plate1 34.0 104.11415
#> 27 ABC039 D3 39(1,D3) X39 plate1 25.5 36.71057
#> 28 ABC040 D4 40(1,D4) X40 plate1 35.0 113.51578
#> 29 ABC041 D5 41(1,D5) X41 plate1 73.5 574.17503
#> 30 ABC042 D6 42(1,D6) X42 plate1 22.0 17.57084
#> 31 ABC043 D7 43(1,D7) X43 plate1 28.5 57.56885
#> 32 ABC044 D8 44(1,D8) X44 plate1 35.5 118.30941
#> 33 ABC045 D9 45(1,D9) X45 plate1 24.0 27.75898
#> 34 ABC046 D10 46(1,D10) X46 plate1 98.0 898.35665
#> 35 ABC047 D11 47(1,D11) X47 plate1 26.0 39.92476
#> 36 ABC048 D12 48(1,D12) X48 plate1 33.0 94.97366
#> 37 ABC049 E1 49(1,E1) X49 plate1 25.5 36.71057
#> 38 ABC050 E2 50(1,E2) X50 plate1 32.0 86.11171
#> 39 ABC051 E3 51(1,E3) X51 plate1 81.5 679.50647
#> 40 ABC052 E4 52(1,E4) X52 plate1 29.5 65.30075
#> 41 ABC053 E5 53(1,E5) X53 plate1 25.0 33.60918
#> 42 ABC054 E6 54(1,E6) X54 plate1 42.0 185.40211
#> 43 ABC055 E7 55(1,E7) X55 plate1 46.5 235.95779
#> 44 ABC056 E8 56(1,E8) X56 plate1 29.0 61.38969
#> 45 ABC057 E9 57(1,E9) X57 plate1 24.0 27.75898
#> 46 ABC058 E10 58(1,E10) X58 plate1 37.0 133.03862
#> 47 ABC059 E11 59(1,E11) X59 plate1 37.5 138.05846
#> 48 ABC060 E12 60(1,E12) X60 plate1 32.5 90.50674
#> 49 ABC061 F1 61(1,F1) X61 plate1 25.5 36.71057
#> 50 ABC062 F2 62(1,F2) X62 plate1 33.5 99.51020
#> 51 ABC063 F3 63(1,F3) X63 plate1 31.0 77.54691
#> 52 ABC064 F4 64(1,F4) X64 plate1 36.5 128.07266
#> 53 ABC065 F5 65(1,F5) X65 plate1 22.0 17.57084
#> 54 ABC066 F6 66(1,F6) X66 plate1 39.0 153.42474
#> 55 ABC067 F7 67(1,F7) X67 plate1 37.5 138.05846
#> 56 ABC068 F8 68(1,F8) X68 plate1 36.0 123.16233
#> 57 ABC069 F9 69(1,F9) X69 plate1 22.0 17.57084
#> 58 ABC070 F10 70(1,F10) X70 plate1 30.0 69.29915
#> 59 ABC071 F11 71(1,F11) X71 plate1 32.0 86.11171
#> 60 ABC072 F12 72(1,F12) X72 plate1 26.0 39.92476
#> 61 ABC073 G1 73(1,G1) X73 plate1 25.5 36.71057
#> 62 ABC074 G2 74(1,G2) X74 plate1 28.5 57.56885
#> 63 ABC075 G3 75(1,G3) X75 plate1 31.0 77.54691
#> 64 ABC076 G4 76(1,G4) X76 plate1 30.0 69.29915
#> 65 ABC077 G5 77(1,G5) X77 plate1 27.0 46.67771
#> 66 ABC078 G6 78(1,G6) X78 plate1 33.0 94.97366
#> 67 ABC079 G7 79(1,G7) X79 plate1 27.5 50.20976
#> 68 ABC080 G8 80(1,G8) X80 plate1 36.0 123.16233
#> 69 ABC081 G9 81(1,G9) X81 plate1 22.0 17.57084
#> 70 ABC082 G10 82(1,G10) X82 plate1 30.0 69.29915
#> 71 ABC083 G11 83(1,G11) X83 plate1 24.5 30.62411
#> 72 ABC084 G12 84(1,G12) X84 plate1 31.0 77.54691
#> 73 ABC085 H1 85(1,H1) X85 plate1 26.5 43.24827
#> 74 ABC086 H2 86(1,H2) X86 plate1 32.0 86.11171
#> 75 ABC087 H3 87(1,H3) X87 plate1 26.0 39.92476
#> 76 ABC088 H4 88(1,H4) X88 plate1 35.0 113.51578
#> 77 ABC089 H5 89(1,H5) X89 plate1 24.0 27.75898
#> 78 ABC090 H6 90(1,H6) X90 plate1 64.0 450.94228
#> 79 ABC091 H7 91(1,H7) X91 plate1 33.5 99.51020
#> 80 ABC092 H8 92(1,H8) X92 plate1 31.5 81.79096
#> 81 ABC093 H9 93(1,H9) X93 plate1 27.0 46.67771
#> 82 ABC094 H10 94(1,H10) X94 plate1 24.0 27.75898
#> 83 ABC095 H11 95(1,H11) X95 plate1 34.5 108.78336
#> 84 ABC096 H12 96(1,H12) X96 plate1 27.5 50.20976
#> PvLDH-ST_DilutionReciprocal PvLDH-ST_MinStd PvLDH-ST_MaxDilution
#> 1 3.016885e-03 30 50.81
#> 2 1.737051e-02 30 50.81
#> 3 1.004922e-02 30 50.81
#> 4 1.161282e-02 30 50.81
#> 5 1.052923e-02 30 50.81
#> 6 1.443019e-02 30 50.81
#> 7 5.934506e-06 30 50.81
#> 8 6.100947e-03 30 50.81
#> 9 4.238046e-03 30 50.81
#> 10 1.161282e-02 30 50.81
#> 11 1.004922e-02 30 50.81
#> 12 9.007870e-04 30 50.81
#> 13 1.628938e-02 30 50.81
#> 14 3.857325e-03 30 50.81
#> 15 5.728305e-03 30 50.81
#> 16 3.322336e-03 30 50.81
#> 17 1.628938e-02 30 50.81
#> 18 1.737051e-02 30 50.81
#> 19 6.986631e-03 30 50.81
#> 20 1.991645e-02 30 50.81
#> 21 6.100947e-03 30 50.81
#> 22 4.463669e-02 30 50.81
#> 23 1.161282e-02 30 50.81
#> 24 2.504711e-02 30 50.81
#> 25 1.104890e-02 30 50.81
#> 26 9.604842e-03 30 50.81
#> 27 2.724011e-02 30 50.81
#> 28 8.809348e-03 30 50.81
#> 29 1.741629e-03 30 50.81
#> 30 5.691249e-02 30 50.81
#> 31 1.737051e-02 30 50.81
#> 32 8.452413e-03 30 50.81
#> 33 3.602438e-02 30 50.81
#> 34 1.113144e-03 30 50.81
#> 35 2.504711e-02 30 50.81
#> 36 1.052923e-02 30 50.81
#> 37 2.724011e-02 30 50.81
#> 38 1.161282e-02 30 50.81
#> 39 1.471656e-03 30 50.81
#> 40 1.531376e-02 30 50.81
#> 41 2.975378e-02 30 50.81
#> 42 5.393682e-03 30 50.81
#> 43 4.238046e-03 30 50.81
#> 44 1.628938e-02 30 50.81
#> 45 3.602438e-02 30 50.81
#> 46 7.516615e-03 30 50.81
#> 47 7.243309e-03 30 50.81
#> 48 1.104890e-02 30 50.81
#> 49 2.724011e-02 30 50.81
#> 50 1.004922e-02 30 50.81
#> 51 1.289542e-02 30 50.81
#> 52 7.808068e-03 30 50.81
#> 53 5.691249e-02 30 50.81
#> 54 6.517854e-03 30 50.81
#> 55 7.243309e-03 30 50.81
#> 56 8.119366e-03 30 50.81
#> 57 5.691249e-02 30 50.81
#> 58 1.443019e-02 30 50.81
#> 59 1.161282e-02 30 50.81
#> 60 2.504711e-02 30 50.81
#> 61 2.724011e-02 30 50.81
#> 62 1.737051e-02 30 50.81
#> 63 1.289542e-02 30 50.81
#> 64 1.443019e-02 30 50.81
#> 65 2.142350e-02 30 50.81
#> 66 1.052923e-02 30 50.81
#> 67 1.991645e-02 30 50.81
#> 68 8.119366e-03 30 50.81
#> 69 5.691249e-02 30 50.81
#> 70 1.443019e-02 30 50.81
#> 71 3.265401e-02 30 50.81
#> 72 1.289542e-02 30 50.81
#> 73 2.312231e-02 30 50.81
#> 74 1.161282e-02 30 50.81
#> 75 2.504711e-02 30 50.81
#> 76 8.809348e-03 30 50.81
#> 77 3.602438e-02 30 50.81
#> 78 2.217579e-03 30 50.81
#> 79 1.004922e-02 30 50.81
#> 80 1.222629e-02 30 50.81
#> 81 2.142350e-02 30 50.81
#> 82 3.602438e-02 30 50.81
#> 83 9.192582e-03 30 50.81
#> 84 1.991645e-02 30 50.81
#> PvLDH-ST_MaxStd PvLDH-ST_MinDilution
#> 1 23757 1e+06
#> 2 23757 1e+06
#> 3 23757 1e+06
#> 4 23757 1e+06
#> 5 23757 1e+06
#> 6 23757 1e+06
#> 7 23757 1e+06
#> 8 23757 1e+06
#> 9 23757 1e+06
#> 10 23757 1e+06
#> 11 23757 1e+06
#> 12 23757 1e+06
#> 13 23757 1e+06
#> 14 23757 1e+06
#> 15 23757 1e+06
#> 16 23757 1e+06
#> 17 23757 1e+06
#> 18 23757 1e+06
#> 19 23757 1e+06
#> 20 23757 1e+06
#> 21 23757 1e+06
#> 22 23757 1e+06
#> 23 23757 1e+06
#> 24 23757 1e+06
#> 25 23757 1e+06
#> 26 23757 1e+06
#> 27 23757 1e+06
#> 28 23757 1e+06
#> 29 23757 1e+06
#> 30 23757 1e+06
#> 31 23757 1e+06
#> 32 23757 1e+06
#> 33 23757 1e+06
#> 34 23757 1e+06
#> 35 23757 1e+06
#> 36 23757 1e+06
#> 37 23757 1e+06
#> 38 23757 1e+06
#> 39 23757 1e+06
#> 40 23757 1e+06
#> 41 23757 1e+06
#> 42 23757 1e+06
#> 43 23757 1e+06
#> 44 23757 1e+06
#> 45 23757 1e+06
#> 46 23757 1e+06
#> 47 23757 1e+06
#> 48 23757 1e+06
#> 49 23757 1e+06
#> 50 23757 1e+06
#> 51 23757 1e+06
#> 52 23757 1e+06
#> 53 23757 1e+06
#> 54 23757 1e+06
#> 55 23757 1e+06
#> 56 23757 1e+06
#> 57 23757 1e+06
#> 58 23757 1e+06
#> 59 23757 1e+06
#> 60 23757 1e+06
#> 61 23757 1e+06
#> 62 23757 1e+06
#> 63 23757 1e+06
#> 64 23757 1e+06
#> 65 23757 1e+06
#> 66 23757 1e+06
#> 67 23757 1e+06
#> 68 23757 1e+06
#> 69 23757 1e+06
#> 70 23757 1e+06
#> 71 23757 1e+06
#> 72 23757 1e+06
#> 73 23757 1e+06
#> 74 23757 1e+06
#> 75 23757 1e+06
#> 76 23757 1e+06
#> 77 23757 1e+06
#> 78 23757 1e+06
#> 79 23757 1e+06
#> 80 23757 1e+06
#> 81 23757 1e+06
#> 82 23757 1e+06
#> 83 23757 1e+06
#> 84 23757 1e+06
#>
# }