fc.pos: fc.pos

In liukf10/TEST: Disease-Drived Differential Proteins and Proteome-Wide Co-Expression Network Associated Analysis

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

rm(list = ls())
library(DDPNA)
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]

liukf10/TEST documentation built on May 20, 2019, 12:59 a.m.