shiftCor {statTarget} | R Documentation

## shiftCor for GUI

### Description

shiftCor provides the QC based signal correction for large scale metabolomics and targeted proteomics.

### Usage

    shiftCor(samPeno, samFile, Frule = 0.8, MLmethod = "QCRFSC",
      ntree = 500, QCspan = 0, degree = 2, imputeM = "KNN",
      coCV = 30, plot = FALSE)

### Arguments

`samPeno` | The file with the meta information including the sample name, batches, class and order.
`samFile` | The file with the expression information.
`Frule` | Modified n precent rule function. A variable will be kept if it has a non-zero value for at least n precent of samples in any one group. (Default: 0.8)
`MLmethod` | The machine learning method for QC based signal correction. i.e. QC based random forest signal correction (QC-RFSC) and QC based LOESS signal correction (QC-RLSC).
`ntree` | Number of trees to grow in random forest model.
`QCspan` | The smoothing parameter for QC-RLSC which controls the bias-variance tradeoff in QC-RLSC method if the QCspan is set at '0', the generalised cross-validation will be performed to avoid overfitting the observed data.
`degree` | Lets you specify local constant regression (i.e., the Nadaraya-Watson estimator, degree=0), local linear regression (degree=1), or local polynomial fits (degree=2, the default) for QC-RLSC.
`imputeM` | The parameter for imputation method i.e., nearest neighbor averaging, 'KNN'; minimum values, 'min'; Half of minimum values, 'minHalf'; median values, 'median'.
`coCV` | Define the cutoff value (0-100) of CV for controlling the number of features.
`plot` | Defines if images of feature quality should be generated (TRUE) or not (FALSE). Defaults to FALSE.

### Value

the shiftCor files. See the details at https://stattarget.github.io

### Examples

    datpath <- system.file('extdata',package = 'statTarget')
    samPeno <- paste(datpath,'MTBLS79_sampleList.csv', sep='/')
    samFile <- paste(datpath,'MTBLS79.csv', sep='/')
    shiftCor(samPeno,samFile, MLmethod = 'QCRFSC', imputeM = 'KNN',coCV = 30)

[Package statTarget version 1.17.4 Index]