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Adding translations for cliqueMS (#141) #157

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Jul 8, 2024
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Adding translations for cliqueMS (#141) #157

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5 changes: 5 additions & 0 deletions R/annotate_masses.R
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Original file line number Diff line number Diff line change
Expand Up @@ -35,18 +35,18 @@
#'
#' @examples NULL
annotate_masses <-
function(features = get_params(step = "annotate_masses")$files$features$prepared,

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filter_nitro = get_params(step = "annotate_masses")$options$nitrogen_rule,

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output_annotations = get_params(step = "annotate_masses")$files$annotations$prepared$structural$ms1,

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output_edges = get_params(step = "annotate_masses")$files$networks$spectral$edges$raw,

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name_source = get_params(step = "annotate_masses")$names$source,
name_target = get_params(step = "annotate_masses")$names$target,
library = get_params(step = "annotate_masses")$files$libraries$sop$merged$keys,

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str_stereo = get_params(step = "annotate_masses")$files$libraries$sop$merged$structures$stereo,

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str_met = get_params(step = "annotate_masses")$files$libraries$sop$merged$structures$metadata,

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str_nam = get_params(step = "annotate_masses")$files$libraries$sop$merged$structures$names,

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str_tax_cla = get_params(step = "annotate_masses")$files$libraries$sop$merged$structures$taxonomies$cla,

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str_tax_npc = get_params(step = "annotate_masses")$files$libraries$sop$merged$structures$taxonomies$npc,

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adducts_list = get_params(step = "annotate_masses")$ms$adducts,
clusters_list = get_params(step = "annotate_masses")$ms$clusters,
neutral_losses_list = get_params(step = "annotate_masses")$ms$neutral_losses,
Expand Down Expand Up @@ -132,13 +132,18 @@
# TODO this should be externalized
adducts_translations <-
c(
"-2H" = "-H2", # cliqueMS
"-3H" = "-H3", # cliqueMS
"-2H2O" = "-H4O2 (2xH2O)", # mzmine
"-3H2O" = "-H6O3 (3xH2O)", # mzmine
"-4H2O" = "-H8O4 (4xH2O)", # mzmine
"-5H2O" = "-H10O5 (5xH2O)", # mzmine
"-NH3" = "+H3N", # mzmine
"+2H" = "+H2", # mzmine
"+2K" = "+K2", # cliqueMS
"+2Na" = "+Na2", # mzmine
"+3K" = "+K3", # cliqueMS
"+3Na" = "+Na3", # cliqueMS
"+Acetate" = "C2H3O2", # mzmine
"+ACN" = "+C2H3N", # mzmine
"+FA" = "CHO2", # mzmine
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