write2file: Print metabCombiner Report to File.

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

Print metabCombiner Report to File.

Description

Prints a combinedTable report to a file, specified by file argument. Output file has an empty line between each separate m/z group for ease of viewing.

Usage

write2file(object, file, sep = ",")

Arguments

object	metabCombiner object or combinedTable
file	character string naming the output file path
sep	Character field separator. Values within each row are separated by this character.

Value

no values returned

Examples

data(plasma30)
data(plasma20)

p30 <- metabData(plasma30, samples = "CHEAR")
p20 <- metabData(plasma20, samples = "Red", rtmax = 17.25)
p.comb <- metabCombiner(xdata = p30, ydata = p20, binGap = 0.0075)

p.comb <- selectAnchors(p.comb, tolmz = 0.003, tolrtq = 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 <- labelRows(p.comb, maxRankX = 2, maxRankY = 2, remove = TRUE)


###using metabCombiner object as input
write2file(p.comb, file = "plasma-combined.csv", sep = ",")

###using combinedTable report and feature data as input
cTable <- combinedTable(p.comb)
write2file(cTable, file = "plasma-combined.txt", sep = "\t")

hhabra/metabCombiner documentation built on Jan. 26, 2024, 12:23 p.m.