exportIL: exportIL

In RogerGinBer/RHermes: Improving metabolome characterization using molecular formula databases

exportIL

Description

Organizes the IL entries into multiple injections taking into account the user-specified parameters. Outputs a single or multiple csv files that serve as input for the MS to performed MSMS analysis.

Usage

exportIL(
  struct,
  id,
  file = "./InclusionList",
  mode = "both",
  maxOver = 5,
  defaultIT = 100,
  sepFiles = FALSE,
  maxInjections = 9999
)

## S4 method for signature 'RHermesExp,numeric'
exportIL(
  struct,
  id,
  file = "./InclusionList",
  mode = "both",
  maxOver = 5,
  defaultIT = 100,
  sepFiles = FALSE,
  maxInjections = 9999
)

Arguments

struct	The RHermesExp object.
id	The IL ID in the RHermesExp object. The IDs are assigned by the order in which the IL are generated.
file	A string containing the folder to save the IL csv/s into and the basename for the file. By default will be your working directory and the default name is 'InclusionList' as in './InclusionList'.
mode	Whether to plan set of continuous MS2 entries (PRM), adaptative injection time scans at the apexes of the entries' peaks or both (which optimizes instrument free time). Options are: "continuous", "deep" or "both".
maxOver	Numeric, very important. It's the number of mz-rt segments that can be monitored at the same time by the MS instrument. Higher numbers lead to less injections but the number of scans for each IL entry will be reduced and gives problems when deconvoluting the MS2 spectras. It is ignored if mode = "deep". Defaults to 5.
defaultIT	Numeric, the default IT in ms for continuous MS2 scans (only aplicable in Orbitrap instruments and for "continuous" and "both" modes). Defaults to 100ms.
sepFiles	Logical, whether to generate a single csv file or multiple csvs, each corresponding to each injection/chromatographic run. From our experience with an Orbitrap Fusion, separate csvs will simplify the task.
maxInjections	Numeric, the maximum number of planned injections to export. Defaults to 9999 to export all of them.

Value

Nothing. As a side effect, it generates one/multiple .csv files with the inclusion list data

Examples

if(FALSE){
   exportIL(myHermes, 1, 'C:/SomeFolder', maxOver = 5, sepFiles = FALSE)
}

RogerGinBer/RHermes documentation built on Nov. 6, 2022, 11:34 a.m.