metaX (version 1.4.0)

metaXpipe: metaXpipe

Description

metaXpipe

Usage

metaXpipe(para, plsdaPara, cvFilter = 0.3, remveOutlier = TRUE, outTol = 1.2, doQA = TRUE, doROC = TRUE, qcsc = FALSE, nor.method = "pqn", pclean = TRUE, t = 1, scale = "uv", idres = NULL, nor.order = 1, out.rmqc = FALSE, saveRds = TRUE, ...)

Arguments

para

A metaXpara object.

plsdaPara

A plsDAPara object.

cvFilter

Filter peaks which cv > cvFilter in QC samples.

remveOutlier

Remove outlier samples.

outTol

The threshold to remove outlier samples.

doQA

Boolean, setting the argument to TRUE will perform plot quality figures.

doROC

A logical indicates whether to calculate the ROC

qcsc

Boolean, setting the argument to TRUE to perform quality control-robust loess signal correction.

nor.method

Normalization method.

pclean

Boolean, setting the argument to TRUE to perform data cleaning

t

Data transformation method. See transformation.

scale

Data scaling method.

idres

A file containing the metabolite identification result

nor.order

The order of normalization, only valid when qcsc is TRUE. 1: before QC-RLSC, 2: after QC-RLSC.

out.rmqc

Boolean, setting the argument to TRUE to remove the QC samples for the csv file.

saveRds

Boolean, setting the argument to TRUE to save some objects to disk for debug. Only useful for developer. Default is TRUE.

...

Other argument

Value

A metaXpara object.

Examples

## Not run: 
# ## example 1: no QC sample
# library(faahKO)
# xset <- group(faahko)
# xset <- retcor(xset)
# xset <- group(xset)
# xset <- fillPeaks(xset)
# peaksData <- as.data.frame(groupval(xset,"medret",value="into"))
# peaksData$name <- row.names(peaksData)
# para <- new("metaXpara")
# rawPeaks(para) <- peaksData
# ratioPairs(para) <- "KO:WT"
# outdir(para) <- "test"
# sampleListFile(para) <- system.file("extdata/faahKO_sampleList.txt", 
#     package = "metaX")
# plsdaPara <- new("plsDAPara")
# p <- metaXpipe(para,plsdaPara=plsdaPara)
# 
# ## example 2: has QC samples
# para <- new("metaXpara")
# pfile <- system.file("extdata/MTBLS79.txt",package = "metaX")
# sfile <- system.file("extdata/MTBLS79_sampleList.txt",package = "metaX")
# rawPeaks(para) <- read.delim(pfile,check.names = FALSE)
# sampleListFile(para) <- sfile
# ratioPairs(para) <- "S:C"
# plsdaPara <- new("plsDAPara")
# p <- metaXpipe(para,plsdaPara=plsdaPara)
# ## End(Not run)