MseekFamily: MseekFamily

In mjhelf/Mosaic: Metaboseek platform

MseekFamily

Description

The MseekFamily of classes includes the MseekFT and MseekGraph S3 classes. Many methods described here will work on both classes

addProcessHistory: adds (appends) a single ProcessHistory object to the .processHistory slot. Copied description and Method template for addProcessHistory from xcms.

processHistory: extract a list of ProcessHistory objects from an object, representing changes made to the object.

previousStep: extract the most recent ProcessHistory object from an object, representing the last recorded changes made to the object.

searchFunParam: extract the ProcessHistory objects which were generated by a function named like fun (looking in the object@param@fun slots from all ProcessHistory objects).

groupingTable, groupingTable<-: Get or set the Mseek intensity column grouping

intensityCols, intensityCols<-: Get or set the Mseek intensity column names

hasAdjustedRtime: check if the object contains retention time correction information.

MseekHash: digests the object (excluding the process history) into a character string

rename: rename a MseekFamily object

FTFilter: apply a list of filters to a MseekFT object

Usage

## S4 method for signature 'MseekFamily,ProcessHistory'
addProcessHistory(object, ph)

## S4 method for signature 'MseekFamily'
processHistory(object)

## S4 method for signature 'MseekFamily'
previousStep(object)

is.MseekFT(x)

is.MseekGraph(x)

is.MseekFamily(x)

## S4 method for signature 'MseekFamily'
searchFunParam(object, fun = "", index = FALSE)

## S4 method for signature 'MseekFamily'
groupingTable(object)

## S4 replacement method for signature 'MseekFamily,data.frame'
groupingTable(object) <- value

## S4 method for signature 'MseekFamily'
intensityCols(object)

## S4 replacement method for signature 'MseekFamily'
intensityCols(object) <- value

## S4 method for signature 'MseekFamily'
hasAdjustedRtime(object)

## S4 method for signature 'MseekFamily'
MseekHash(object)

## S4 method for signature 'MseekFamily'
rename(object, name)

## S4 method for signature 'MseekFT'
FTFilter(object, filters = list(), sortBy = character(), decreasing = TRUE)

Arguments

object	an MseekFT object.
ph	a ProcessHistory object
x	object to test for class
fun	character(1), function name to look for
index	get index in list instead of actual value
value	for groupingTable<-: a data.frame with columns Column and Group. For intensityCols<-: a character vector of column names
name	file path to write to
filters	a list of filters
sortBy	sort by this column
decreasing	logical to specify if sort should be decreasing.

Value

The addProcessHistory method returns the input object with the provided ProcessHistory appended to the process history.

For hasAdjustedRtime: A logical, indicating if the object contains retention time correction information.

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