data-raw/HST_Explorer_WhiteList.R

In hemoshear/assayr2: Tools for analyzing assay data

#' ----
#' title: PureHoney white list
#' description: List of allowed values to standardize data flowing into the HST Explorer
#' author: nathan.day@hemoshear.com
#' -----

library(magrittr)

### White List -------------------------------------------------------------
# populated from existing nate_db values
white_list <- list(
  "isotope" = c("C13", "C12"),
  "tx_challenge" = c(
    "13C-ILE", "13C-ILE+12C-KIVA", "13C-KIVA",
    "13C-KIVA-ABT", "13C-KIVA+12C-ILE", "13C-KIVA+13C-ILE",
    "13C-KMV", "13C-VAL", "MeD3-KMV", "3-OH-Isobutyryl",
    "S-KMVA", "12C-R-KMVA", "13C-Methionine", "12C-KIVA+12C-ILE",
    "13C-Propionate", "12C-KIVA+13C-Acetate_1mM",
    "12C-KIVA+13C-Acetate", "12C-KIVA+13C-Butyrate",
    "12C-Propionate+13C-Acetate", "13C-ILE+H004666+H003579"
  ),
  "media" = c(
    "Corning_lowAA_highLEU", "Corning_lowAA_highLEU_noILE_noVAL",
    "DMEM_low_AA_highLEU_noFBS", "DMEM_lowAA_highLEU", "DMEM_lowAA_highLEU_noVAL_noILE_noFBS",
    "DMEM_lowAA_lowGlucose_highLEU", "DMEM_lowAA_lowGlucose_highLEU_10%FBS",
    "DMEM_lowAA_lowGlucose_highLEU_noFBS", "RPMI"
  ),
  "donor" = c("16020", "Aja", "HUH7", "Jo", "Jurkat", "TJ", "Rat", "Human"),
  "curve_plot" = c(
    "EHA", "Acetyl", "Free", "Isobutyryl", "Methacrylyl",
    "Methacylyl", "2-Methylbutyryl", "Methylmalonyl", "Propionyl",
    "Tiglyl", "3-OH-Isobutyryl", "2-OH-2-Methylbutyrate", "2-Methylcitrate",
    "3-OH-Propionyl"
  ),
  "targ" = c(
    "12C-Acetyl", "12C-Isobutyryl", "12C-Methacrylyl", "12C-2-Methylbutyryl",
    "12C-Methylmalonyl", "12C-Propionyl", "12C-Tiglyl", "12C2-EHA", "13C-Acetyl",
    "13C-EHA", "13C-Isobutyryl", "13C-Methacrylyl", "13C-Methacylyl",
    "13C-2-Methylbutyryl", "13C-Methylmalonyl", "13C-Propionyl", "13C-Tiglyl",
    "Free", "MeD3-Acetyl", "MeD3-Propionyl", "MeD8-Methylbutyryl",
    "12C-3-OH-Isobutyryl", "13C-2-OH-2-Methylbutyrate", "13C-2-Methylcitrate",
    "12C-2-OH-2-Methylbutyrate", "12C-2-Methylcitrate", "13C-3-OH-Propionyl",
    "12C-3-OH-Propionyl"
  )
)

white_list$curve_plot %<>% c(., paste0(., "-Car"))
white_list$targ %<>% c(., paste0(., "-Car"))