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