MsList-class: Virtual class for MSsary list like objects

In thomasp85/MSsary: LC-MS/MS analysis in R

Description

This class defines the storage and general methods for extracted MS data within the MSsary framework. The class is virtual and must be sublassed for use with e.g. scans (MsScanList). Data is stored efficiently in a single matrix, and the class itself takes care of indexing individual elements. Furthermore it retains a link to the MsConnections from where the data was extracted.

Usage

## S4 method for signature 'MsList'
length(x)

## S4 method for signature 'MsList'
names(x)

## S4 method for signature 'MsList'
uNames(object)

## S4 method for signature 'MsList,numeric,missing,missing'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'MsList,logical,missing,missing'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'MsList,numeric,missing'
x[[i, j]]

## S4 method for signature 'MsList'
c(x, y, ..., recursive = FALSE)

## S4 method for signature 'MsList'
sort(x, decreasing = FALSE, by, ...)

## S4 method for signature 'MsList'
isEmpty(object)

## S4 method for signature 'MsList'
dropEmpty(object)

## S4 method for signature 'MsList'
isRaw(object)

## S4 method for signature 'MsList'
msInfo(object)

## S4 method for signature 'MsList'
msData(object)

Arguments

x	An MsList object

Methods (by generic)

• length: Number of elements in the object

• names: Get the names of the elements

• uNames: Get unique names of elements

• [: Subset an MsList object

• [: Subset an MsList object

• [[: Extract raw data

• c: Combine multiple lists

• sort: Sort an MsList by a property

• isEmpty: See if elements are empty

• dropEmpty: Removes empty elements

• isRaw: See if elements are based on raw values

• msInfo: Get the info for each element as a data.frame

• msData: Get the data as a list of matrices

Slots

connections

A list of MsConnections objects

info

A data.frame with information pertaining to each element (metadata)

data

A matrix holding the actual data

mapping

A matrix giving start and end indexes in @data for each row in @info. Additionally it also contains the index for the MsConnections object in the @connections list

thomasp85/MSsary documentation built on May 31, 2019, 11:11 a.m.