spectrumFilter {clippda} | R Documentation

## A function to filter out samples with conflicting pair-wise compound information

### Description

This function filters out samples whose spectra have poor pairwise correlations. These samples give conflicting TIC information.

### Usage

    spectrumFilter(Data,threshold,no.peaks)

### Arguments

`Data` | a data frame of duplicate peak data, in the format of "raw .csv" data from the Biomarker wizard. The original data frame to have the following columns: `SampleTag`, `CancerType`, `Spectrum.`, `Peak`. `Intensity` and `Substance.Mass`.
`threshold` | indicates the threshold for rejecting samples whose spectra contain conflicting signal information.
`no.peaks` | the number of peaks.

### Value

A data frame with two columns: the first contains the IDs of the samples meeting the threshold and the second contains the corresponding correlations (i.e. similarities in peak information across spectra).

### Author(s)

Stephen Nyangoma

### References

Ward DG, Nyangoma S, Joy H, Hamilton E, Wei W, Tselepis C, Steven N, Wakelam MJ, Johnson PJ, Ismail T, Martin A: Proteomic profiling of urine for the detection of colon cancer. Proteome Sci. 2008, 16(6):19

### Examples

    #######################################################
    #######################################################

    data(liverRawData) # raw version of liverdata
    ############################################################################################
    ############################################################################################
    # These samples pre-processed to:
    #  (i) discard the information on samples which have no replicate data, and
    # (ii) for samples with more than 2 replicate expression data, only duplicates with most
    #      similar peak information are retained for use in subsequent analyses.
    # A wrapper function for executing these two pre-processing steps is preProcRepeatedPeakData
    #############################################################################################
    #############################################################################################

    threshold <- 0.80
    no.replicates <- 2
    no.peaks <- 53
    Data <- preProcRepeatedPeakData(liverRawData, no.peaks, no.replicates, threshold)

    head(spectrumFilter(Data,threshold,no.peaks))

[Package clippda version 1.42.0 Index]