metaXpipe: metaXpipe

In wenbostar/metaX: A flexible and comprehensive software for processing omics data.

metaXpipe

Description

metaXpipe

Usage

metaXpipe(para, plsdaPara, cvFilter = 0.3, remveOutlier = TRUE,
  outTol = 1.2, doQA = TRUE, doROC = TRUE, qcsc = 0,
  nor.method = "pqn", pclean = TRUE, t = 1, scale = "uv",
  idres = NULL, center = TRUE, nor.order = 1, out.rmqc = FALSE,
  saveRds = TRUE, cpu = 0, missValueRatioQC = 0.5,
  missValueRatioSample = 0.8, pcaLabel = "none", classCol = NULL,
  ...)

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	QC-based batch correction, 0=none,1=QC-RLSC(Quality control-robust loess signal correction),2=SVR(SVR normalization).
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-based batch correction, 2: after QC-based batch correction.
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.
cpu	The number of cpu used, default is all available cpus.
missValueRatioQC	The cutoff of the ratio of miss value for the features in QC, default is 0.5.
missValueRatioSample	The cutoff of the ratio of miss value for the features in sample, default is 0.8.
pcaLabel	The label used for PCA score plot, "none","order" and "sample" are supported. Default is "none"
...	Other argument

Value

A metaXpara object.

Author(s)

Bo Wen [e-mail]

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)

wenbostar/metaX documentation built on July 4, 2023, 7:50 p.m.