constructRawLayout: constructRawLayout

In mjhelf/Mosaic: Metaboseek platform

constructRawLayout

Description

Constructor function for the rawLayout S3 class, holding information on MSdata grouping and layout options in Metaboseek.

Usage

constructRawLayout(rawgrouptable, stem = NULL, msnExp = NULL)

Arguments

rawgrouptable	a data.frame with columns File and Group , holding file paths and group names, respectively.
stem	if the file paths in rawgrouptable are not full (e.g. subdirectories of the working directory), this should be the path of the working directory.
msnExp	if not NULL, must be an OnDiskMSnExp object, see details

Details

If msnExp is provided, will generate an element called MSnExp_summary in the resulting rawLayout which is a data.frame containing information that can be used for normalization. Columns in MSnExp_summary:

• sampleNamesFile names of raw files

• bpmeans mean values of the basepeak intensity for each file

• ticmeans mean values of the TIC intensity for each file

• normfactor_bp normalization factor for each file based on base peak

• normfactor_tic normalization factor for each file based on TIC intensity peak

Multiplying all intensity values for each file with their normfactors will yield the same mean intensity for all files.

Value

a rawLayout object

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