buildMseekFT: buildMseekFT

In mjhelf/Mosaic: Metaboseek platform

buildMseekFT

Description

Methods to build an MseekFT object from an xsAnnotate, xcmsSet or data.frame object, and to load or save MseekFT objects

loadMseekFT: load a MseekFT object from an .mskFT file

saveMseekFT: save a MseekFT object to a file, registering the save event in the processHistory

Usage

## S4 method for signature 'xsAnnotate'
buildMseekFT(object, processHistory = list(), ...)

## S4 method for signature 'XCMSnExp'
buildMseekFT(object, processHistory = list(), ...)

## S4 method for signature 'data.frame'
buildMseekFT(
  object,
  processHistory = list(),
  anagrouptable = NULL,
  from = "auto",
  ...
)

## S4 method for signature 'character'
loadMseekFT(object)

## S4 method for signature 'MseekFT'
saveMseekFT(object, file, writeCSV = FALSE, writeRDS = TRUE)

Arguments

object	an xsAnnotate, xcmsSet or data.frame object. For saveMseekFT, an MseekFT object, for loadMseekFT a charcater vector of file paths
processHistory	a list of processHistory objects, will override the processHistory list that may be supplied by object
...	additional arguments passed to constructFeatureTable
anagrouptable	Analysis grouping table: a data.frame with columns "Column" (containing column names from df with intensity values) and "Group" (defining a group for each entry in "Column")
from	input format. If auto, will run .getFTFormat to determine the format.
file	file path to write to
writeCSV	write object to a .csv file (data frame only)
writeRDS	write object to an .mskFT (RDS) file; saves the entire object

Value

an object of class MseekFT, with processHistory extended from object if applicable.

the MseekFT object, with saving event added to processHistory

mjhelf/Mosaic documentation built on April 28, 2022, 11:32 a.m.