update (entropy)

taxonomicallyinformedannotation · Jul 29, 2023 · 5e890d9 · 5e890d9
1 parent 4269d0e
commit 5e890d9
Showing 1 changed file with 0 additions and 147 deletions.
diff --git a/inst/pipelines/_targets.R b/inst/pipelines/_targets.R
@@ -1332,26 +1332,11 @@ list(
  x = par_ann_spe$files$annotations$raw$spectral,
  fixed = TRUE
  ),
- method = par_ann_spe$annotations$ms2$method,
  threshold = par_ann_spe$annotations$ms2$thresholds$similarity,
  ppm = par_ann_spe$ms$tolerances$mass$ppm$ms2,
  dalton = par_ann_spe$ms$tolerances$mass$dalton$ms2,
- npeaks = par_ann_spe$
- annotations$
- ms2$
- thresholds$
- peaks$
- absolute,
- rpeaks = par_ann_spe$
- annotations$
- ms2$
- thresholds$
- peaks$
- ratio,
- condition = par_ann_spe$annotations$ms2$thresholds$condition,
  qutoff = par_ann_spe$ms$intensity$thresholds$ms2,
  parallel = par_ann_spe$options$parallel,
- fast = par_ann_spe$options$fast,
  approx = par_ann_spe$annotations$ms2$approx,
  parameters = par_ann_spe
  )
@@ -1370,26 +1355,11 @@ list(
  x = par_ann_spe$files$annotations$raw$spectral,
  fixed = TRUE
  ),
- method = par_ann_spe$annotations$ms2$method,
  threshold = par_ann_spe$annotations$ms2$thresholds$similarity,
  ppm = par_ann_spe$ms$tolerances$mass$ppm$ms2,
  dalton = par_ann_spe$ms$tolerances$mass$dalton$ms2,
- npeaks = par_ann_spe$
- annotations$
- ms2$
- thresholds$
- peaks$
- absolute,
- rpeaks = par_ann_spe$
- annotations$
- ms2$
- thresholds$
- peaks$
- ratio,
- condition = par_ann_spe$annotations$ms2$thresholds$condition,
  qutoff = par_ann_spe$ms$intensity$thresholds$ms2,
  parallel = par_ann_spe$options$parallel,
- fast = par_ann_spe$options$fast,
  approx = par_ann_spe$annotations$ms2$approx,
  parameters = par_ann_spe
  )
@@ -1437,26 +1407,11 @@ list(
  x = par_ann_spe$files$annotations$raw$spectral,
  fixed = TRUE
  ),
- method = par_ann_spe$annotations$ms2$method,
  threshold = par_ann_spe$annotations$ms2$thresholds$similarity,
  ppm = par_ann_spe$ms$tolerances$mass$ppm$ms2,
  dalton = par_ann_spe$ms$tolerances$mass$dalton$ms2,
- npeaks = par_ann_spe$
- annotations$
- ms2$
- thresholds$
- peaks$
- absolute,
- rpeaks = par_ann_spe$
- annotations$
- ms2$
- thresholds$
- peaks$
- ratio,
- condition = par_ann_spe$annotations$ms2$thresholds$condition,
  qutoff = par_ann_spe$ms$intensity$thresholds$ms2,
  parallel = par_ann_spe$options$parallel,
- fast = par_ann_spe$options$fast,
  approx = par_ann_spe$annotations$ms2$approx,
  parameters = par_ann_spe
  )
@@ -1475,26 +1430,11 @@ list(
  x = par_ann_spe$files$annotations$raw$spectral,
  fixed = TRUE
  ),
- method = par_ann_spe$annotations$ms2$method,
  threshold = par_ann_spe$annotations$ms2$thresholds$similarity,
  ppm = par_ann_spe$ms$tolerances$mass$ppm$ms2,
  dalton = par_ann_spe$ms$tolerances$mass$dalton$ms2,
- npeaks = par_ann_spe$
- annotations$
- ms2$
- thresholds$
- peaks$
- absolute,
- rpeaks = par_ann_spe$
- annotations$
- ms2$
- thresholds$
- peaks$
- ratio,
- condition = par_ann_spe$annotations$ms2$thresholds$condition,
  qutoff = par_ann_spe$ms$intensity$thresholds$ms2,
  parallel = par_ann_spe$options$parallel,
- fast = par_ann_spe$options$fast,
  approx = par_ann_spe$annotations$ms2$approx,
  parameters = par_ann_spe
  )
@@ -1550,34 +1490,15 @@ list(
  output = par_cre_edg_spe$files$networks$spectral$edges$raw,
  name_source = par_cre_edg_spe$names$source,
  name_target = par_cre_edg_spe$names$target,
- method = par_cre_edg_spe$annotations$ms2$method,
  threshold = par_cre_edg_spe$
  annotations$
  ms2$
  thresholds$
  similarity,
  ppm = par_cre_edg_spe$ms$tolerances$mass$ppm$ms2,
  dalton = par_cre_edg_spe$ms$tolerances$mass$dalton$ms2,
- npeaks = par_cre_edg_spe$
- annotations$
- ms2$
- thresholds$
- peaks$
- absolute,
- rpeaks = par_cre_edg_spe$
- annotations$
- ms2$
- thresholds$
- peaks$
- ratio,
- condition = par_cre_edg_spe$
- annotations$
- ms2$
- thresholds$
- condition,
  qutoff = par_cre_edg_spe$ms$intensity$thresholds$ms2,
  parallel = par_cre_edg_spe$options$parallel,
- fast = par_cre_edg_spe$options$fast,
  parameters = par_cre_edg_spe
  )
  }
@@ -2180,34 +2101,15 @@ list(
  output = "data/interim/benchmark/benchmark_edges_spe_pos.tsv.gz",
  name_source = def_cre_edg_spe$names$source,
  name_target = def_cre_edg_spe$names$target,
- method = def_cre_edg_spe$annotations$ms2$method,
  threshold = def_cre_edg_spe$
  annotations$
  ms2$
  thresholds$
  similarity,
  ppm = def_cre_edg_spe$ms$tolerances$mass$ppm$ms2,
  dalton = def_cre_edg_spe$ms$tolerances$mass$dalton$ms2,
- npeaks = def_cre_edg_spe$
- annotations$
- ms2$
- thresholds$
- peaks$
- absolute,
- rpeaks = def_cre_edg_spe$
- annotations$
- ms2$
- thresholds$
- peaks$
- ratio,
- condition = def_cre_edg_spe$
- annotations$
- ms2$
- thresholds$
- condition,
  qutoff = 0,
  parallel = TRUE,
- fast = FALSE,
  parameters = def_cre_edg_spe
  )
  }
@@ -2220,34 +2122,15 @@ list(
  output = "data/interim/benchmark/benchmark_edges_spe_neg.tsv.gz",
  name_source = def_cre_edg_spe$names$source,
  name_target = def_cre_edg_spe$names$target,
- method = def_cre_edg_spe$annotations$ms2$method,
  threshold = def_cre_edg_spe$
  annotations$
  ms2$
  thresholds$
  similarity,
  ppm = def_cre_edg_spe$ms$tolerances$mass$ppm$ms2,
  dalton = def_cre_edg_spe$ms$tolerances$mass$dalton$ms2,
- npeaks = def_cre_edg_spe$
- annotations$
- ms2$
- thresholds$
- peaks$
- absolute,
- rpeaks = def_cre_edg_spe$
- annotations$
- ms2$
- thresholds$
- peaks$
- ratio,
- condition = def_cre_edg_spe$
- annotations$
- ms2$
- thresholds$
- condition,
  qutoff = 0,
  parallel = TRUE,
- fast = FALSE,
  parameters = def_cre_edg_spe
  )
  }
@@ -2370,26 +2253,11 @@ list(
  library = lib_spe_is_lot_pre_pos,
  polarity = "pos",
  output = "data/interim/benchmark/benchmark_ann_spe_pos.tsv.gz",
- method = def_ann_spe$annotations$ms2$method,
  threshold = def_ann_spe$annotations$ms2$thresholds$similarity,
  ppm = def_ann_spe$ms$tolerances$mass$ppm$ms2,
  dalton = def_ann_spe$ms$tolerances$mass$dalton$ms2,
- npeaks = def_ann_spe$
- annotations$
- ms2$
- thresholds$
- peaks$
- absolute,
- rpeaks = def_ann_spe$
- annotations$
- ms2$
- thresholds$
- peaks$
- ratio,
- condition = def_ann_spe$annotations$ms2$thresholds$condition,
  qutoff = 0,
  parallel = TRUE,
- fast = def_ann_spe$options$fast,
  approx = def_ann_spe$annotations$ms2$approx,
  parameters = def_ann_spe
  )
@@ -2403,26 +2271,11 @@ list(
  library = lib_spe_is_lot_pre_neg,
  polarity = "neg",
  output = "data/interim/benchmark/benchmark_ann_spe_neg.tsv.gz",
- method = def_ann_spe$annotations$ms2$method,
  threshold = def_ann_spe$annotations$ms2$thresholds$similarity,
  ppm = def_ann_spe$ms$tolerances$mass$ppm$ms2,
  dalton = def_ann_spe$ms$tolerances$mass$dalton$ms2,
- npeaks = def_ann_spe$
- annotations$
- ms2$
- thresholds$
- peaks$
- absolute,
- rpeaks = def_ann_spe$
- annotations$
- ms2$
- thresholds$
- peaks$
- ratio,
- condition = def_ann_spe$annotations$ms2$thresholds$condition,
  qutoff = 0,
  parallel = TRUE,
- fast = def_ann_spe$options$fast,
  approx = def_ann_spe$annotations$ms2$approx,
  parameters = def_ann_spe
  )