reliabilityCheckSwath: A function to check the coverage, fdr distrubtions,...
In SwathXtend: SWATH extended library generation and statistical data analysis

1	reliabilityCheckSwath(seed.swathfile, ext.swathfile, max.fdrpass = 3, max.peptide = 2)

`seed.swathfile`	A string representing the Swath results obtained using the seed library. The Swath result file should be a PeakView extracted Excel (.xlsx) file with six tabs: "Area - ions", "Area - peptides", "Area - proteins", "Score", "FDR" and "Observed RT". The SWATH result checking functions require that worksheet “Area - peptides" and “FDR" must exist.
`ext.swathfile`	A string representing the Swath results obtained using the extended library. The Swath result file should be a PeakView extracted Excel (.xlsx) file with six tabs: “Area - ions", “Area - peptides", “Area - proteins", “Score", “FDR" and “Observed RT". The SWATH result checking functions require that worksheet “Area - peptides" and “FDR" must exist.
`max.fdrpass`	A numeric value representing the maximum number of samples that pass the fdr threshold (0.01)
`max.peptide`	A numeric value representing the maximum number of peptides in a protein as a filter

`fdr.bins`	a matrix of the FDR percentage in each of the 8 bins
`dat.comb`	a matrix of the various numbers as the SWATH filtering threshold changes. These numbers include protein, peptide, median correlation, cv and bland altman mesuarement.

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files <- paste(system.file("files",package="SwathXtend"), 
		c("Swath_result_Lib2.xlsx", "Swath_result_Lib2_3.xlsx"), sep="/")
res = reliabilityCheckSwath(files[1], files[2])