uafR

uafR - A new standard for mass spectrometry data processing

Objective

An R package that automates GC-MS processing.

Installation

When made public, you can install the development version of uafR from GitHub with:

# install.packages("devtools")
devtools::install_github("castratton/uafR")

Example Mass Spectrometry Workflows

These are basic examples of how to use core functions. The input .CSV file has strict column name/input data requirements. The column names MUST include: ‘Component.RT’, ‘Component.Area’, ‘Base.Peak.MZ’, ‘File.Name’, ‘Compound.Name’, and ‘Match.Factor’ in no particular order.

library(uafR)

input_dat = read.csv("your/gcms/dataset.csv")

Component.RT | Base.Peak.MZ | Component.Area | Compound.Name | Match.Factor | File.Name
:————-:|:—————-:|:—————-:|:—————————|:————–:|:————: 8.229034 |84.00 |906.4701 |Pipradrol |62.62271 |Std_soln_07
8.286703 |120.00 |209705.1878 |Methyl salicylate |98.16152 |Std_soln_00a
8.296408 |119.99 |30332.9022 |Methyl salicylate |95.79911 |Std_soln_00
8.303958 |120.00 |6476.4785 |Methyl salicylate |86.29569 |Std_soln_07
8.348031 |105.00 |420.8119 |3-Hexen-1-ol, benzoate, (Z)-|68.78156 |Std_soln_00
… |… |… |… |… |…

In this example, the user knows what chemicals they are interested in:

input_spread = spreadOut(input_dat)
query_chemicals = c("Linalool", "Methyl Salicylate", "Limonene", "alpha-Thujene")

### extract the query_chemicals from the "spread out" input:
input_exacto = mzExacto(input_spread, query_chemicals)

In this example, the user just wants to keep the top hits:

query_chemicals = input_dat$Compound.Name[input_dat$Match.Factor > 80]

input_exacto = mzExacto(input_spread, query_chemicals)

Example Cheminformatics Workflow

## example usage for chemical informatics:
query_chemicals = c("Linalool", "Methyl Salicylate", "Limonene", "alpha-Thujene")
GroupA = c("Guaiacol",	"Tridecane",	"Ethyl heptanoate", "Caffeine")
GroupB = c("2-Aminothiazole", "Aspirin", "Octanoic acid", "alpha-Pinene", "Toluene")
chem_library = data.frame(cbind(GroupA, GroupB))

query_categorated = categorate(query_chemicals, chem_library, input_format = "wide")

Combined Mass Spectrometry + Cheminformatics Workflow

query_chemicals = input_dat$Compound.Name[input_dat$Match.Factor > 70]
query_categorated = categorate(query_chemicals, chem_library, input_format = "wide")

## example of using the info from categorate() to get a user-defined set of chemicals with exactoThese():
these_chems = exactoThese(query_categorated, subsetBy = "Database", subsetArgs = "All")
these_chems = exactoThese(query_categorated, subsetBy = "Database", subsetArgs = "reactives")
these_chems = exactoThese(query_categorated, subsetBy = "Database", subsetArgs = "LOTUS")
these_chems = exactoThese(query_categorated, subsetBy = "Database", subsetArgs = "KEGG")
these_chems = exactoThese(query_categorated, subsetBy = "Database", subsetArgs = "FEMA")
these_chems = exactoThese(query_categorated, subsetBy = "Database", subsetArgs = "FDA_SPL")
these_chems = exactoThese(query_categorated, subsetBy = "Database", subsetArgs = c("reactives", "FEMA"))
these_chems = exactoThese(query_categorated, subsetBy = "FMCS", subsetArgs = "MW", subsetArgs2 = "Greater Than", subset_input = 125)
these_chems = exactoThese(query_categorated, subsetBy = "FMCS", subsetArgs = "MW", subsetArgs2 = "Less Than", subset_input = 205)
these_chems = exactoThese(query_categorated, subsetBy = "FMCS", subsetArgs = "MW", subsetArgs2 = "Between", subset_input = c(125, 200))
these_chems = exactoThese(query_categorated, subsetBy = "FMCS", subsetArgs = "Rings", subsetArgs2 = "Greater Than", subset_input = 1)
these_chems = exactoThese(query_categorated, subsetBy = "FMCS", subsetArgs = "Groups", subsetArgs2 = "Greater Than", subset_input = 2)
these_chems = exactoThese(query_categorated, subsetBy = "FMCS", subsetArgs = "Atoms", subsetArgs2 = "Greater Than", subset_input = 6)
these_chems = exactoThese(query_categorated, subsetBy = "FMCS", subsetArgs = "NCharges", subsetArgs2 = "Greater Than", subset_input = 2)
these_chems = exactoThese(query_categorated, subsetBy = "Library", subsetArgs = "GroupB")

input_exacto = mzExacto(input_spread, these_chems)