The goal of padlocdev is to simplify the validation of padloc-db data, ensuring that the system models, HMMs, and metadata will work together as expected when running padloc.
Vignettes
Explore the available vignettes for more information on the capabilities of padlocdev and typical workflows for processing padloc-db data.
| Vignette | Description |
|---|---|
vignette("reading-data") |
Learn how to read padloc-db data into R |
vignette("validating-data") |
Learn how to validate padloc-db data |
vignette("preparing-data") |
Learn how to prepare padloc-db data for use |
vignette("workflow") |
A summarised workflow of padloc-db validation |
Example files
This package includes example files for demonstrating functions.
These files can be listed and accessed with the function
padlocdev_example(). In the following code, you’ll see this
function used to access these example files.
If file = ... is not specified,
padlocdev_example() lists all example files (these are
located in the package directory
padlocdev/inst/exdata/).
padlocdev_example()
#> [1] "padloc-db"
#> [2] "padloc-db/hmm"
#> [3] "padloc-db/hmm/PDLC00150.hmm"
#> [4] "padloc-db/hmm/PDLC00151.hmm"
#> [5] "padloc-db/hmm/PDLC00174.hmm"
#> [6] "padloc-db/hmm/PDLC00175.hmm"
#> [7] "padloc-db/hmm/PDLC00195.hmm"
#> [8] "padloc-db/hmm/PDLC00196.hmm"
#> [9] "padloc-db/hmm/PDLC00199.hmm"
#> [10] "padloc-db/hmm/PDLC00200.hmm"
#> [11] "padloc-db/hmm/PDLC00202.hmm"
#> [12] "padloc-db/hmm/PDLC00203.hmm"
#> [13] "padloc-db/hmm/PDLC02171.hmm"
#> [14] "padloc-db/hmm/PDLC02172.hmm"
#> [15] "padloc-db/hmm/PDLC02173.hmm"
#> [16] "padloc-db/hmm/PDLC02174.hmm"
#> [17] "padloc-db/hmm/PDLC02175.hmm"
#> [18] "padloc-db/hmm/PDLC02176.hmm"
#> [19] "padloc-db/hmm/PDLC02177.hmm"
#> [20] "padloc-db/hmm/PDLC02178.hmm"
#> [21] "padloc-db/hmm/PDLC02181.hmm"
#> [22] "padloc-db/hmm/PDLC02182.hmm"
#> [23] "padloc-db/hmm/PDLC02437.hmm"
#> [24] "padloc-db/hmm/PDLC02438.hmm"
#> [25] "padloc-db/hmm/PDLC02459.hmm"
#> [26] "padloc-db/hmm/PDLC02460.hmm"
#> [27] "padloc-db/hmm/PDLC02471.hmm"
#> [28] "padloc-db/hmm/PDLC02472.hmm"
#> [29] "padloc-db/hmm/PDLC02494.hmm"
#> [30] "padloc-db/hmm/PDLC02495.hmm"
#> [31] "padloc-db/hmm/PDLC02496.hmm"
#> [32] "padloc-db/hmm/PDLC02497.hmm"
#> [33] "padloc-db/hmm/PDLC02500.hmm"
#> [34] "padloc-db/hmm/PDLC02501.hmm"
#> [35] "padloc-db/hmm/PDLC02504.hmm"
#> [36] "padloc-db/hmm/PDLC02505.hmm"
#> [37] "padloc-db/hmm/PDLC02506.hmm"
#> [38] "padloc-db/hmm/PDLC02510.hmm"
#> [39] "padloc-db/hmm/PDLC02511.hmm"
#> [40] "padloc-db/hmm/PDLC02512.hmm"
#> [41] "padloc-db/hmm/PDLC02513.hmm"
#> [42] "padloc-db/hmm/PDLC02515.hmm"
#> [43] "padloc-db/hmm/PDLC02516.hmm"
#> [44] "padloc-db/hmm/PDLC02541.hmm"
#> [45] "padloc-db/hmm/PDLC02542.hmm"
#> [46] "padloc-db/hmm_meta.txt"
#> [47] "padloc-db/sys"
#> [48] "padloc-db/sys/DRT_class_I.yaml"
#> [49] "padloc-db/sys/DRT_class_II.yaml"
#> [50] "padloc-db/sys/DRT_class_III.yaml"
#> [51] "padloc-db/sys/DRT_other.yaml"
#> [52] "padloc-db/sys/DRT_type_I.yaml"
#> [53] "padloc-db/sys/DRT_type_II.yaml"
#> [54] "padloc-db/sys/DRT_type_III.yaml"
#> [55] "padloc-db/sys/DRT_type_IV.yaml"
#> [56] "padloc-db/sys/DRT_type_V.yaml"
#> [57] "padloc-db/sys/brex_other.yaml"
#> [58] "padloc-db/sys/brex_type_I.yaml"
#> [59] "padloc-db/sys/brex_type_II.yaml"
#> [60] "padloc-db/sys/brex_type_III.yaml"
#> [61] "padloc-db/sys/brex_type_IV.yaml"
#> [62] "padloc-db/sys/brex_type_V.yaml"
#> [63] "padloc-db/sys/brex_type_VI.yaml"
#> [64] "padloc-db/sys/hachiman_other.yaml"
#> [65] "padloc-db/sys/hachiman_type_I.yaml"
#> [66] "padloc-db/sys/hachiman_type_II.yaml"
#> [67] "padloc-db/sys_groups.txt"
#> [68] "padloc-db/sys_meta.txt"
#> [69] "padloc-db-broken"
#> [70] "padloc-db-broken/hmm"
#> [71] "padloc-db-broken/hmm/PDLC00150.hmm"
#> [72] "padloc-db-broken/hmm/PDLC00151.hmm"
#> [73] "padloc-db-broken/hmm/PDLC00174.hmm"
#> [74] "padloc-db-broken/hmm/PDLC00175.hmm"
#> [75] "padloc-db-broken/hmm/PDLC00195.hmm"
#> [76] "padloc-db-broken/hmm/PDLC00196.hmm"
#> [77] "padloc-db-broken/hmm/PDLC00199.hmm"
#> [78] "padloc-db-broken/hmm/PDLC00200.hmm"
#> [79] "padloc-db-broken/hmm/PDLC00202.hmm"
#> [80] "padloc-db-broken/hmm/PDLC00203.hmm"
#> [81] "padloc-db-broken/hmm/PDLC02171.hmm"
#> [82] "padloc-db-broken/hmm/PDLC02172.hmm"
#> [83] "padloc-db-broken/hmm/PDLC02173.hmm"
#> [84] "padloc-db-broken/hmm/PDLC02174.hmm"
#> [85] "padloc-db-broken/hmm/PDLC02175.hmm"
#> [86] "padloc-db-broken/hmm/PDLC02176.hmm"
#> [87] "padloc-db-broken/hmm/PDLC02177.hmm"
#> [88] "padloc-db-broken/hmm/PDLC02178.hmm"
#> [89] "padloc-db-broken/hmm/PDLC02181.hmm"
#> [90] "padloc-db-broken/hmm/PDLC02182.hmm"
#> [91] "padloc-db-broken/hmm/PDLC02438.hmm"
#> [92] "padloc-db-broken/hmm/PDLC02459.hmm"
#> [93] "padloc-db-broken/hmm/PDLC02460.hmm"
#> [94] "padloc-db-broken/hmm/PDLC02471.hmm"
#> [95] "padloc-db-broken/hmm/PDLC02472.hmm"
#> [96] "padloc-db-broken/hmm/PDLC02494.hmm"
#> [97] "padloc-db-broken/hmm/PDLC02496.hmm"
#> [98] "padloc-db-broken/hmm/PDLC02497.hmm"
#> [99] "padloc-db-broken/hmm/PDLC02500.hmm"
#> [100] "padloc-db-broken/hmm/PDLC02501.hmm"
#> [101] "padloc-db-broken/hmm/PDLC02504.hmm"
#> [102] "padloc-db-broken/hmm/PDLC02505.hmm"
#> [103] "padloc-db-broken/hmm/PDLC02506.hmm"
#> [104] "padloc-db-broken/hmm/PDLC02512.hmm"
#> [105] "padloc-db-broken/hmm/PDLC02513.hmm"
#> [106] "padloc-db-broken/hmm/PDLC02515.hmm"
#> [107] "padloc-db-broken/hmm/PDLC02516.hmm"
#> [108] "padloc-db-broken/hmm/PDLC02541.hmm"
#> [109] "padloc-db-broken/hmm/PDLC02542.hmm"
#> [110] "padloc-db-broken/hmm/PDLC03000.hmm"
#> [111] "padloc-db-broken/hmm/PDLC04000.hmm"
#> [112] "padloc-db-broken/hmm/PDLC05000.hmm"
#> [113] "padloc-db-broken/hmm_meta.txt"
#> [114] "padloc-db-broken/sys"
#> [115] "padloc-db-broken/sys/DRT_class_I.yaml"
#> [116] "padloc-db-broken/sys/DRT_class_II.yaml"
#> [117] "padloc-db-broken/sys/DRT_class_III.yaml"
#> [118] "padloc-db-broken/sys/DRT_other.yaml"
#> [119] "padloc-db-broken/sys/DRT_type_I.yaml"
#> [120] "padloc-db-broken/sys/DRT_type_III.yaml"
#> [121] "padloc-db-broken/sys/DRT_type_IV.yaml"
#> [122] "padloc-db-broken/sys/DRT_type_V.yaml"
#> [123] "padloc-db-broken/sys/brex_other.yaml"
#> [124] "padloc-db-broken/sys/brex_type_I.yaml"
#> [125] "padloc-db-broken/sys/brex_type_III.yaml"
#> [126] "padloc-db-broken/sys/brex_type_IV.yaml"
#> [127] "padloc-db-broken/sys/brex_type_V.yaml"
#> [128] "padloc-db-broken/sys/brex_type_VI.yaml"
#> [129] "padloc-db-broken/sys/generic_system_A.yaml"
#> [130] "padloc-db-broken/sys/generic_system_B.yaml"
#> [131] "padloc-db-broken/sys/hachiman_other.yaml"
#> [132] "padloc-db-broken/sys/hachiman_type_I.yaml"
#> [133] "padloc-db-broken/sys_groups.txt"
#> [134] "padloc-db-broken/sys_meta.txt"Otherwise, the full path to the file is generated.
padlocdev_example(file = "padloc-db/hmm/PDLC00150.hmm")
#> /home/runner/work/_temp/Library/padlocdev/extdata/padloc-db/hmm/PDLC00150.hmm