Relabel column names to Standardised Naming Convention
Source:R/readSeroData.R
dot-relabel_columns.RdThis is a helper function to be used inside `readSeroData()` to relabel columns for each plate.
Examples
# \donttest{
your_raw_data <- system.file("extdata", "example_MAGPIX_plate1.csv", package = "SeroTrackR")
if (
requireNamespace("dplyr", quietly = TRUE) &&
requireNamespace("janitor", quietly = TRUE)
) {
# Read in raw luminex file
df <- .read_luminex_file(your_raw_data)
# Get the start and end rows of the data section: start = "Median", end = "Net MFI"
row1 <- which(df$xPONENT == "Median")
row2 <- which(df$xPONENT == "Net MFI")
# Apply data processing pipeline, including .relabel_columns()
df |>
dplyr::slice((row1 + 1):(row2 - 1)) |>
janitor::row_to_names(row_number = 1) |>
janitor::clean_names() |>
dplyr::select(dplyr::where(~ !all(is.na(.x)))) |>
dplyr::filter(dplyr::if_any(dplyr::everything(), ~ !is.na(.x))) |>
dplyr::mutate(dplyr::across(everything(), ~ gsub("NaN", 0, .))) |>
.relabel_columns()
}
#> Warning: Row 1 does not provide unique names. Consider running clean_names() after row_to_names().
#> location sample EBP LF005 LF010 LF016 MSP8 RBP2b.P87
#> 1 1(1,A1) Blank1 20 200 20 10 20 10
#> 2 2(1,A2) Blank2 15 291 15 15 15 10
#> 3 3(1,A3) S1 15710.5 11990 22583 21244 24306 7907.5
#> 4 4(1,A4) S2 13545 8285 16947.5 16146 17172 7186
#> 5 5(1,A5) S3 9767 4950 10865 10621.5 11358 4475.5
#> 6 6(1,A6) S4 5648.5 2519 6060 5968.5 6237 3508
#> 7 7(1,A7) S5 4104.5 1431 3711.5 3738 3883.5 2082
#> 8 8(1,A8) S6 2105 676.5 1889 1667 2136 1102
#> 9 9(1,A9) S7 1107 328 1106 890 1204 657
#> 10 10(1,A10) S8 452.5 141 465 405.5 522 277
#> 11 11(1,A11) S9 209 65 206.5 181.5 249 138
#> 12 12(1,A12) S10 105 42 113.5 87 134 93
#> 13 13(1,B1) Unknown013 2712 1569 673 327 182 1068
#> 14 14(1,B2) Unknown014 134 378 117 197 58 465.5
#> 15 15(1,B3) Unknown015 182 209 208 374 221.5 463
#> 16 16(1,B4) Unknown016 152 229.5 101 89 48 591
#> 17 17(1,B5) Unknown017 1135 236 299 507 209.5 671
#> 18 18(1,B6) Unknown018 174 395 175 78 70 103
#> 19 19(1,B7) Unknown019 421 2081.5 529 149 962 1441.5
#> 20 20(1,B8) Unknown020 24 49 22 13 15.5 14
#> 21 21(1,B9) Unknown021 24 45 22 13 16 13
#> 22 22(1,B10) Unknown022 21464 11789 2508.5 8001 2342 1386
#> 23 23(1,B11) Unknown023 795 6135.5 407 273 535.5 1575
#> 24 24(1,B12) Unknown024 1574 348.5 892 288 306 590
#> 25 25(1,C1) Unknown025 146 408.5 1130.5 83 100 301
#> 26 26(1,C2) Unknown026 1330.5 3036 965 174 79 1090
#> 27 27(1,C3) Unknown027 358 4074.5 335.5 140 390 6704
#> 28 28(1,C4) Unknown028 481 1870 421 182.5 1777.5 2390
#> 29 29(1,C5) Unknown029 551 1282 331.5 165 77 244
#> 30 30(1,C6) Unknown030 943 584.5 235 135 3017 1034
#> 31 31(1,C7) Unknown031 532.5 1533 315 210 2575.5 2903
#> 32 32(1,C8) Unknown032 768 12605 409 7632 9860 13703
#> 33 33(1,C9) Unknown033 130 239.5 72 64 37 156
#> 34 34(1,C10) Unknown034 40 60 37 25 26.5 23.5
#> 35 35(1,C11) Unknown035 167 605 253 329 3973 1426.5
#> 36 36(1,C12) Unknown036 1879 4562 415 18287 11482.5 12031
#> 37 37(1,D1) Unknown037 256 1507 117 129 168 488
#> 38 38(1,D2) Unknown038 24 49 22 12 15 14
#> 39 39(1,D3) Unknown039 384 1708 326 1172.5 986 1041
#> 40 40(1,D4) Unknown040 210 512 221 191 89 203
#> 41 41(1,D5) Unknown041 351.5 312 165.5 88 66 205
#> 42 42(1,D6) Unknown042 1278 5810 275 230.5 137 2032
#> 43 43(1,D7) Unknown043 318 397 130 130.5 78 903
#> 44 44(1,D8) Unknown044 493.5 2980.5 401 5932.5 3536 4699.5
#> 45 45(1,D9) Unknown045 9686 873 333 166 791 1093
#> 46 46(1,D10) Unknown046 777.5 581 241.5 173 1479.5 899
#> 47 47(1,D11) Unknown047 455 416.5 126 67 48 400
#> 48 48(1,D12) Unknown048 202 1142 137.5 176 204.5 1090
#> 49 49(1,E1) Unknown049 333.5 623.5 368 10430 2340 4375
#> 50 50(1,E2) Unknown050 561 7984 441 128 141 1993
#> 51 51(1,E3) Unknown051 506.5 340 152.5 147 90 600
#> 52 52(1,E4) Unknown052 254 367 392.5 89 142.5 280
#> 53 53(1,E5) Unknown053 888 1955 438 173 507 1009
#> 54 54(1,E6) Unknown054 426 1877 186 9767 15945 10073
#> 55 55(1,E7) Unknown055 5733 1301.5 1920.5 220.5 4833 2340
#> 56 56(1,E8) Unknown056 19092 14422 1993 12836.5 7426 11930
#> 57 57(1,E9) Unknown057 596 15139 371.5 229 535.5 14032
#> 58 58(1,E10) Unknown058 1028 2646 1486 292 9357 8009
#> 59 59(1,E11) Unknown059 512 4735 3408 127.5 191 4401
#> 60 60(1,E12) Unknown060 883 1953 755 586 122 830
#> 61 61(1,F1) Unknown061 977 8719 509 187 1289 12930
#> 62 62(1,F2) Unknown062 791 1944 465 216.5 12307 5029
#> 63 63(1,F3) Unknown063 397 987 924 133 79 253
#> 64 64(1,F4) Unknown064 1111 613 357 196 8496 7914
#> 65 65(1,F5) Unknown065 956 2369 644 389 8762 9649
#> 66 66(1,F6) Unknown066 1307 20590 1335 10780 12736 25375.5
#> 67 67(1,F7) Unknown067 433 382 173 105 59 480
#> 68 68(1,F8) Unknown068 161 279 2524.5 105.5 55 307
#> 69 69(1,F9) Unknown069 439 732.5 397 2108 9692 8090
#> 70 70(1,F10) Unknown070 1837 11406 467.5 20011 19606 24476.5
#> 71 71(1,F11) Unknown071 244 1665.5 166 124 154 224
#> 72 72(1,F12) Unknown072 482 3990.5 388 3736 7436 7361
#> 73 73(1,G1) Unknown073 656 3103 505 14386 2343 5503
#> 74 74(1,G2) Unknown074 243 568.5 693 141 79 339
#> 75 75(1,G3) Unknown075 1409.5 1123 379 153 167.5 1013
#> 76 76(1,G4) Unknown076 467.5 6741 238 174 181 6160
#> 77 77(1,G5) Unknown077 329 630 196 119 278 787
#> 78 78(1,G6) Unknown078 1122.5 17810 677 12254 16011 18719
#> 79 79(1,G7) Unknown079 10853 817.5 255 189 2247.5 3322
#> 80 80(1,G8) Unknown080 743.5 820 313.5 289 9351.5 7171
#> 81 81(1,G9) Unknown081 723 1255 299 253 95 712
#> 82 82(1,G10) Unknown082 168 684 131 198 135.5 392
#> 83 83(1,G11) Unknown083 180 276 205 4646.5 2550 2664.5
#> 84 84(1,G12) Unknown084 249.5 4104 250 96 68 1020
#> 85 85(1,H1) Unknown085 479 190 105 131 66 1449
#> 86 86(1,H2) Unknown086 164 327 234.5 66 75.5 259
#> 87 87(1,H3) Unknown087 281.5 1794 413 75 469.5 802
#> 88 88(1,H4) Unknown088 269 1067 141 7595 14464 7592
#> 89 89(1,H5) Unknown089 3247 382 470 98 2319.5 2009
#> 90 90(1,H6) Unknown090 20593 14902.5 2021 10184 5805.5 14083.5
#> 91 91(1,H7) Unknown091 395 9914 211 131.5 325 3021
#> 92 92(1,H8) Unknown092 904.5 1871 793 172 6106 2093
#> 93 93(1,H9) Unknown093 323 2007.5 1950 106 191 2411
#> 94 94(1,H10) Unknown094 706 2087 791 169 66 990
#> 95 95(1,H11) Unknown095 323 4950 264 107 645 7092
#> 96 96(1,H12) Unknown096 367 1067 259 101 7423 1203
#> 97
#> PTEX150 PvCSS total_events x x_2 x_3 x_4 x_5 x_6
#> 1 30 20 1898
#> 2 20 15 1805
#> 3 13207 12427 1842
#> 4 8550 8034 2044
#> 5 5329 4990 1815
#> 6 2671 2446.5 1950
#> 7 1548 1299 1991
#> 8 698.5 581 1827
#> 9 333 264 2095
#> 10 156 111 1643
#> 11 77 46.5 1888
#> 12 40 28 1876
#> 13 936 223 1927
#> 14 122 93 1965
#> 15 293 868 1970
#> 16 109 110 1911
#> 17 1665.5 266 1977
#> 18 294.5 92 1902
#> 19 241 282 1913
#> 20 28 17 1828
#> 21 29 17 1885
#> 22 1992 2927 2133
#> 23 8821 998 1670
#> 24 315 366 1955
#> 25 652 130 1873
#> 26 179 92 2173
#> 27 8814 5627 2012
#> 28 2465 411 1794
#> 29 579 229 2023
#> 30 4928 7730 1893
#> 31 2779 7300 1946
#> 32 5612 6383 1843
#> 33 204 49 1900
#> 34 40 27 1947
#> 35 803 1670 1826
#> 36 4830.5 4217 1690
#> 37 908 87 1988
#> 38 29 17 1943
#> 39 299.5 149 1963
#> 40 410 174.5 2159
#> 41 200 183 2122
#> 42 1762 1241 1997
#> 43 1513.5 325 1916
#> 44 574 5389 2026
#> 45 417.5 262 1691
#> 46 1504 260 2044
#> 47 183 61 1639
#> 48 504 459 1957
#> 49 1650 7801.5 1836
#> 50 2147 1502 1963
#> 51 2178 170 1856
#> 52 298 138 2019
#> 53 709 2040 2009
#> 54 1585.5 1124 1964
#> 55 5329 2369 1905
#> 56 4826 3468.5 2052
#> 57 7928.5 1414.5 1712
#> 58 3736 14370.5 1862
#> 59 11567 2923.5 1718
#> 60 425.5 121 1767
#> 61 13891 9531 1735
#> 62 4157 760 1804
#> 63 2317.5 1080.5 1705
#> 64 5772.5 13202 2026
#> 65 6437 21113 1871
#> 66 5493 7696 1868
#> 67 655 367 1813
#> 68 681.5 472.5 2070
#> 69 9513 7341 1870
#> 70 5822 5127.5 2055
#> 71 718 115 1798
#> 72 4111.5 2819 1831
#> 73 357.5 1215 1816
#> 74 2080 1470 1821
#> 75 1553 1738 1979
#> 76 1660.5 1087 1910
#> 77 2052.5 2221 1752
#> 78 3551 10222.5 1670
#> 79 590 258 1702
#> 80 3062 676.5 1739
#> 81 396 129.5 1574
#> 82 292 254.5 1597
#> 83 724 2707 1546
#> 84 960 672 1710
#> 85 1724.5 108 2102
#> 86 260 89 1895
#> 87 345 744.5 1694
#> 88 804.5 467 1817
#> 89 1521 1258 1615
#> 90 4307.5 3073 1452
#> 91 4608 1073.5 1537
#> 92 1303 6595.5 1852
#> 93 7377.5 1699 1563
#> 94 261 65 1472
#> 95 8856 5330 1467
#> 96 1841.5 335 1654
#> 97
# }