updateTables: Update 'metabCombiner' Objects

In hhabra/Combiner: Method for Combining LC-MS Metabolomics Feature Measurements

Update metabCombiner Objects

Description

This method updates the feature list (featData) and aligned table (combinedTable) within a metabCombiner object. Manual changes to the (combinedTable) as well as unmatched X & Y dataset features can be incorporated into the object and the corresponding results. This function is typically paired with link{reduceTable} or other forms of table reduction performed by the user.

Usage

updateTables(object, xdata = NULL, ydata = NULL, combinedTable = NULL)

Arguments

object	metabCombiner object to be updated
xdata	metabData or metabCombiner object originally used to construct the object argument
ydata	metabData or metabCombiner object originally used to construct the object argument
combinedTable	merged table which may be altered by the user. This must have the combinedTable format to be valid (see: ?isCombinedTable)

Details

There are two points where features can be removed from the combinedTable report: during m/z grouping and during the table reduction step. It is also possible for user-specified changes to the report to remove certain features entirely. This function allows for the missed features to be brought back into the table as non-matched entities. For xdata features, the Y columns will be entirely missing values, and ydata features will have missing X information. The feature data (featData) will also be updated for use in subsequent alignments, but only features present in the representative dataset will be retained by default.

Value

metabCombiner object with updates to combinedTable to include features that have been missed or changes by the user.

Note

Duplicated sample & extra column names cannot be copied from the original data they feature in, therefore they are left as missing values.

Examples

data(plasma30)
data(plasma20)
p30 <- metabData(plasma30, samples = "CHEAR")
p20 <- metabData(plasma20, samples = "Red")
p.comb <- metabCombiner(xdata = p30, ydata = p20, xid = "p30", yid = "p20",
                        binGap = 0.0075)

##extracting, modifying, and updating combinedTable
cTable <- combinedTable(p.comb)
cTable <- dplyr::filter(cTable, rty < 17.25)
p.comb <- updateTables(p.comb, combinedTable = cTable)

p.comb <- selectAnchors(p.comb, tolmz = 0.003, tolQ = 0.3, windy = 0.02)
p.comb <- fit_gam(p.comb, k = 20, iterFilter = 1)
p.comb <- calcScores(p.comb, A = 90, B = 14, C = 0.5)
p.comb <- reduceTable(p.comb, delta = 0.2, maxRTerr = 0.5)

##updating to include features removed from xdata & ydata
p.comb <- updateTables(p.comb, xdata = p30, ydata = p20)

#view results
cTable <- combinedTable(p.comb)
fdata <- featData(p.comb)

hhabra/Combiner documentation built on June 5, 2024, 10:56 a.m.