MS analysis in R

Description Details Fields Methods See Also

This class takes care of the communication with the sary database and the raw datafile. Its main responsibility is to ensure a stable connection across sessions without causing the session to crash (This would normally happen if an mzRramp object was accessed in a different session than the one it is created in). It relies on knowledge of the location of the raw and database files and will throw an error if these files are moved.

TODO: Schema for updating file location vs. creating a new object (which is cheap). Decide whether this class also should handle writing to the sary db.

rawFile: The path to the location of the MS raw data file
ramp: Object of class mzRramp. A connection to the MS raw data file
saryFile: The path to the location of the sary database file
saryDB: An SQLiteConnection object. A connection to the sary database

addData(name, data): Adds data to an already created table. 'name' specifies the name of the table, 'data' is a data.frame containing the data to be added.
addTable(name, definition, rtree = FALSE): Creates the table 'name' with the columns defined in 'definition'. The definition can be a character vector that will be concatenated with ', '.
getPeaks(ids): Extract peaks from database
getScans(ids, raw = FALSE): Transparently extract scans, getting modified scans if they exists or read from the raw file if they don't
mzR(): Get the mzRramp connection in a safe manner
removeScans(ids, value = TRUE): Remove scans from the set
resetScans(ids): Reset the state of scans back to its original value
sary(): Get the sary database connection in a safe manner
setData(name, data, key): Insert or update data depending on the existence of key
setScans(ids, scans): Set scans to new values
updateData(name, data, key): Updates column in already existing data
validate(subset = 10): Checks that the header data matches between raw and sary
verify(): Verify that the default tables are present and their structure conforms