fc.pos {DDPNA}R Documentation

fc.pos

Description

Pick up proteins based on foldchange and return proteins position in data.

Usage

fc.pos(fc, vs.set2, vs.set1 = "WT",
       cutoff = 1, datatype = c("none", "log2"),
       fctype = "all", order = TRUE)

Arguments

fc

proteomic data of mean value in groups.

vs.set2

compared group 2 name

vs.set1

compared group 1 name

cutoff

a numberic value indicated foldchange threshold.

datatype

The quantification data is normal data or log2 data. This must be (an abbreviation of) one of the strings "none","log2".

fctype

foldchange is ordered by up-regulated or down-regulated or changed

order

a logical value indicated that whether ordered by foldchange.

Author(s)

Kefu Liu

Examples

data(imputedData)
data <- imputedData
relative <- data$relative_value
rownames(relative) <- data$inf$ori.ID
group <- gsub("[0-9]+", "", colnames(relative))
datamean <- groupmean(relative, group, name = FALSE)
fc_1vs2 <- fc.pos(datamean, vs.set2 = "ad", vs.set1 = "ctl",
                  cutoff = 1, datatype = "none",
                  fctype = "up", order = TRUE)
fc_ID <- rownames(relative)[fc_1vs2]



[Package DDPNA version 0.3.1 Index]