calc_minfrac: Calculate minimum fraction of features across sample classes
In jmosl01/LUMA: LCMS-Based Untargeted Metabolomics Assistant

Description Usage Arguments Value Examples

Calculates the fraction of samples within each class that contains a given feature. Only the minimum fraction across all sample classes is returned.

1	calc_minfrac(Sample.df, xset4, BLANK, Peak.list)

`Sample.df`	a data frame with class info as columns. Must contain a separate row entry for each unique sex and class combination. Must contain the columns `"Sex","Class","n","Endogenous"`.
`xset4`	an xcms object that has had peak picking, retention time alignment, peak grouping, and imputing missing values performed
`BLANK`	a logical indicating whether blanks are being evaluated
`Peak.list`	a table of class 'tbl_df',tbl' or 'data.frame' with variables as columns. Should contain all output columns from `XCMS` and `CAMERA`, and additional columns from `match_Annotation()`.

data frame containing the original table with one additional column 'Minfrac' at the end, followed by the CAMERA columns 'isotopes','adduct','pcgroup'

  library(LUMA)
  if(require(lcmsfishdata, quietly = TRUE)) {
  file <- system.file('extdata','XCMS_objects_Pos.Rdata', package =
  "lcmsfishdata") # is case sensitive on Linux
  load(file)
  # case sensitive on Linux
  file2 <- system.file('extdata','Sample_Class.txt', package = "LUMA") # is
  Sample.df <- read.table(file2, sep = "\t", header = TRUE)
  Peak.list <- lcmsfishdata::Peaklist_Pos$From_CAMERA
  test <- calc_minfrac(Sample.df = Sample.df, xset4 = xset4, BLANK = FALSE,
  Peak.list = Peak.list)
  test[["MinFrac"]][11:23]
  }