quantification.accuracy: Measurment of quantification accuracy of two Swath results

In SwathXtend: SWATH extended library generation and statistical data analysis

Usage

quantification.accuracy(dswat1, dswat2, Sample = NULL, method = c("cor", "cv", "bland.altman"), 
cor.method=c('pearson', 'spearman', 'kendall'), log = FALSE)

Arguments

dswat1	A data frame of peptide peak area of the first Swath result
dswat2	A data frame of peptide peak area of the second Swath result
Sample	A vector of strings representing the sample names of the Swath result
method	A string as one of "cor", "cv" and "bland.altman"
cor.method	A string as one of "pearson", "spearman", and "kendall"
log	A logical value indicating if the peak area will be log transformed before calculating the measurement. Default value is FALSE which means the peak area will not be transformed.

Value

A list of two numeric vectors

vcor	The measurment for the quanitification accuarcy for the same sample
rcor	The measurment for the quanitification accuarcy for the randomised sample

Examples

fswaths = paste(system.file("files",package="SwathXtend"),c("Swath_result_Lib2.xlsx", "Swath_result_Lib2_3.xlsx"), sep="/")

fdr.seed = readWorkbook(fswaths[1], sheet='FDR')
fdr.ext = readWorkbook(fswaths[2], sheet='FDR')
 
swa.seed = readWorkbook(fswaths[1], 2)
swa.ext = readWorkbook(fswaths[2], 2)

fdr.seed = fdr.crit(fdr.seed)
fdr.ext = fdr.crit(fdr.ext)

res = quantification.accuracy(swa.seed[fdr.seed$nfdr.pass >= 2,], swa.ext[fdr.ext$nfdr.pass >= 2,], method="cv")
								

SwathXtend documentation built on Nov. 8, 2020, 6:42 p.m.