Skip to contents

Fic end-to-end workflow (!!!)

Source: R/Fic_workflow.R
ras.Fic_workflow.Rd

Currently not functional!

Usage

ras.Fic_workflow(
  source = c("Waters", "Sciex"),
  ID = "Sample_ID",
  values = "Conc.",
  Buffer = "HBSS",
  Dilution_type = "[:digit:]x",
  Dilution_extract = "[:digit:]+(?=x)",
  stab = "Stab",
  czero = "Czero",
  prot_cell_value = "mg_Protein",
  prot_cell_type = "Cells",
  prot_hom_value = "Protein_conc._mg/mL",
  prot_hom_type = "hom",
  V.medium = 200,
  MassBalance_2.5 = 1.75,
  .compound = "Analyte Peak Name",
  .checkValues = TRUE,
  prot_.split = "Sample Text",
  .summarize = TRUE,
  .SD = TRUE
)

Arguments

source

Data source ("Sciex" or "Waters").

ID

Column name for ID column after splitting.

values

Column name for numeric values.

Buffer

Regex used to select buffer values.

Dilution_type

Regex used to select dilution-factor values.

Dilution_extract

Regex used to extract the dilution factor.

stab

Regex used to select stability values.

czero

Regex used to select C-zero values.

prot_cell_value

Column name for values

prot_cell_type

RegEx to filter by

prot_hom_value

RegEx to filter by

prot_hom_type

RegEx to filter by

V.medium

RegEx to filter by

MassBalance_2.5

Factor for calculating Mass Balance 10.2.5.

.compound

Column name for compounds to prefix Sample_ID, NULL => "Analyte Peak Name"

.checkValues

Removes "<" from the values column to make sure it can be coerced to numeric.

prot_.split

Column name to split for samples in protein dataframe

.summarize

Summarize the data into unique rows in grouping column. Drops the original value columns.

.SD

Create column with Standard Deviation

Value

Data frame with all variables used and calculated.

Examples

if (interactive()) {
  ras.Fic_workflow(source = "Sciex")
}