extract_level1_fup_uc: Extract level 1 ultracentrifugation redgrave1975separationinvitroTKstats data from wide level 0 file

Description

This function extracts data from a Microsoft Excel file containing many columns corresponding to different types of data.

Usage

extract_level1_fup_uc(
  data.set,
  chem.name,
  area.col.num,
  ISTD.name,
  ISTD.offset = 2,
  analysis.method = "GC",
  instrument = "Something or Other 3000",
  inst.param.offset = -3,
  conc.offset = -2,
  area.base = "Area...",
  inst.param.base = "RT...",
  conc.base = "Final Conc....",
  id.cols = c("Name", "Data File", "Acq. Date-Time"),
  type.indicator.col = "Name",
  AF.type.str = "AF",
  T1.type.str = "T1",
  T5.type.str = "T5",
  CC.type.str = "CC"
)

Value

data.frame: A data.frame in standardized "level1" format

Arguments

data.set: (Data Frame) A data frame containing a sheet of data for conversion.
chem.name: (Character) A string giving the lab name of the chemical analyzed. The value provided is used for all rows in the output data frame.
area.col.num: (Numeric) An integer indicating which column of data.set contains the MS feature area for the chemical.
ISTD.name: (Character) A string indicating the internal standard used. The value provided is used for all rows in the output data frame.
ISTD.offset: (Numeric) An integer indicating how many columns difference there is between the chemical of study MS area and the ISTD MS area. (Defaults to 2.)
analysis.method: (Character) A string describing the chemical analysis method. The value provided is used for all rows in the output data frame. (Defaults to "GC", that is gas chromatography.)
instrument: (Character) A string describing the instrument used for chemical analysis. The value provided is used for all rows in the output data frame. (Defaults to "Something or Other 3000".)
inst.param.offset: (Numeric) An integer indicating the difference in the number of columns between the MS peak area and the column giving the instrument parameters. (Defaults to -3.)
conc.offset: (Numeric) An integer indicating the difference in the number of columns between the MS peak area and the column giving the intended concentration for calibration curves. (Defaults to -2.)
area.base: (Character) A character string used for forming the name of MS feature area column names (used for both test chemical and ISTD). (Defaults to "Area...".)
inst.param.base: (Character) A character string used for forming the name of the chemical analysis instrument parameter column name. (Defaults to "RT...".)
conc.base: (Character) A character string used for forming the name of the calibration curve intended concentration column name. (Defaults to "Final Conc....".)
id.cols: (Character Vector) A vector of character strings used for identifying each sample. (Defaults to c("Name", "Data File", "Type", "Acq. Date-Time").)
type.indicator.col: (Character) A character string indicating which column of data.set contains the type of observation. (Defaults to "Name".)
AF.type.str: (Character) String used to annotate observation of this type: Aqueous Fraction. (Defaults to "AF".)
T1.type.str: (Character) String used to annotate observation of this type: Whole Plasma T1h Sample. (Defaults to "T1".)
T5.type.str: (Character) String used to annotate observation of this type: Whole Plasma T5h Sample. (Defaults to "T5".)
CC.type.str: (Character) String used to annotate observation of this type: Calibration Curve. (Defaults to "CC".)

Author

John Wambaugh

Details

The data frame of observations should be annotated according to of these types:

Calibration Curve

Ultracentrifugation Aqueous Fraction

Whole Plasma T1h Sample

References

redgrave1975separationinvitroTKstats