connect_lumadb: Connects to LUMA database

In USEPA/LUMA: LCMS-Based Untargeted Metabolomics Assistant

Description

Establishes a connection to an RSQLite database for combining Peak.lists together from two different ionization modes. Must have previously saved SQLite databases to hard disk.

Usage

connect_lumadb(db.list, db.dir, new.db, mem)

Arguments

db.list	list character names of databases containing results from processing positive mode and negative mode data for samples and blanks
db.dir	character directory containing the databases
new.db	character what should the new database be called.
mem	logical should database be in-memory. Default is FALSE

Value

list of Formal class SQLiteConnections, starting with new.db entry followed by one for each db.list entry

Examples

library(LUMA)
if(require(RSQLite, quietly = TRUE)) {
file <- system.file("extdata","Sample_Data.csv", package =  "LUMA") # is case sensitive on Linux
sample_data <- read.table(file, header = TRUE, sep = ",")
mzdatafiles <- sample_data$CT.ID
samples.pos <- gen_filebase(mzdatafiles = mzdatafiles, BLANK = FALSE, IonMode
= "Positive", ion.id = c("Pos","Neg")) #Returns "Peaklist_Pos" samples.neg <-
gen_filebase(mzdatafiles = mzdatafiles, BLANK = FALSE, IonMode = "Negative",
ion.id = c("Pos","Neg")) #Returns "Peaklist_Neg" blanks.pos <-
gen_filebase(mzdatafiles = mzdatafiles, BLANK = TRUE, IonMode = "Positive",
ion.id = c("Pos","Neg")) #Returns "Blanks_Pos" blanks.neg <-
gen_filebase(mzdatafiles = mzdatafiles, BLANK = TRUE, IonMode = "Negative",
ion.id = c("Pos","Neg")) #Returns "Blanks_Neg"

spos_db <- connect_peakdb(file.base = samples.pos, mem = TRUE)
sneg_db <- connect_peakdb(file.base = samples.neg, mem = TRUE)
bpos_db <- connect_peakdb(file.base = blanks.pos, mem = TRUE)
bneg_db <- connect_peakdb(file.base = blanks.neg, mem = TRUE)
new_db.list <- connect_lumadb(db.list = c("spos_db","sneg_db","bpos_db","bneg_db"), mem = TRUE)
all(sapply(new_db.list, function(x) { #All valid databases are created
  dbIsValid(x)
}))
all(sapply(new_db.list, dbDisconnect))
}

USEPA/LUMA documentation built on Aug. 29, 2020, 1:40 p.m.