Find_FAME_Standards: Scans over a list of input files and annotates FAME standards

In rramaker/CooperR2DGC: Multiple peak alignment for untargeted 2D-GCMS metabolomics analysis (Cooper Lab specific)

Description

Scans over a list of input files and annotates FAME standards

Usage

Find_FAME_Standards(inputFileList, FAME_Frame = system.file("extdata",
  "FIND_FAME_FRAME.txt", package = "CooperR2DGC"), RT1Penalty = 1,
  RT2Penalty = 10, similarityCutoffWarningThreshold = 80)

Arguments

inputFileList	Vector of file paths to scan for FAME standards
RT1Penalty	Penalty used for first retention time errors. Defaults to 1.
RT2Penalty	Penalty used for first retention time errors. Defaults to 10.
similarityCutoffWarningThreshold	Similarity score threshold at which to print a warning for user to double check FAME peak for a sample. Defaults to 85.
FAME_frame	A parsed FAME standard reference file (find at system.file("extdata", "FIND_FAME_FRAME.txt", package="CooperR2DGC"))

Value

Will write out new files with properly annotated FAME standards with the extention _FAME_appended.txt added to the end of the file path

rramaker/CooperR2DGC documentation built on May 28, 2019, 3:30 a.m.