spectrumFilter: A function to filter out samples with conflicting pair-wise...

In clippda: A package for the clinical proteomic profiling data analysis

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))

clippda documentation built on Nov. 8, 2020, 8:13 p.m.