Title — CalciumHarmony • foundrHarmony

There are minor differences among metabolite files. To harmonize, we assume the following: Some number of rows (3-4) at top of file are skipped Columns from “compound” to “data_type” precede mouse data Mouse ID always begins with FFF-nn with “FFF” = founder, “nn” = animal (the rest of Mouse ID seems to change from file to file)

Usage

CalciumHarmony(dataset, links, basal = FALSE, ...)

EnrichHarmony(dataset, links, annot, ...)

Enrich3Harmony(dataset, links, annot, ...)

LipidHarmony(
  dataset,
  links,
  annot,
  sheetNum,
  skipNum,
  minCol,
  maxCol,
  charCols,
  ...
)

LivEnrichHarmony(dataset, links, annot, ...)

MetHarmony(dataset, links, annot, skiprows = 4, ...)

PhysioHarmony(dataset, links, annot, sheet = 2, rename_function, ...)

ProteinHarmony(dataset, links, ...)

moduleHarmony(
  datasetname,
  links,
  object,
  responsename = names(object[[1]]),
  ...,
  datatraits = FALSE,
  traitparams = FALSE
)

Arguments

dataset: name of dataset
links: data frame with links (not used yet)
basal: include `basal` dataset if `TRUE`
...: additional parameters ignored
annot: annotation data frame
sheetNum, skipNum, minCol, maxCol, charCols: additional parameters
skiprows: number of rows to skip
sheet, rename_function: additional parameters
datasetname: name to give to dataset (here for compatibility)
object: object of class traitModule
responsename: name of response to extract
datatraits: incorporate `dataset` into `trait` if `TRUE`
traitparams: incorporate key `params` into `trait` if `TRUE`

Value

data frame

data frame with columns for strain,sex,animal,condition,trait,value

data frame

harmonize object