stat.log2: stat.log2

In DWLS: Gene Expression Deconvolution Using Dampened Weighted Least Squares

stat.log2

Description

One of the functions required for the differential expression analysis using MAST (DEAnalysisMast()) function.

Usage

stat.log2(data.m, group.v, pseudo.count)

Arguments

data.m	Data
group.v	Groupings
pseudo.count	A pseudocount value

Value

A dataframe of the log2 applied results

Examples

#dataSC
#url <- "https://github.com/sistia01/DWLS/raw/main/inst/extdata/dataSC.RData"
#dest <- "data/dataSC.RData"
#load(download.file(url, tempfile(data/dataSC.RData))
#load("dataSC.RData")
#SOLUTION
load(system.file("extdata", "dataSC.RData", package = "DWLS"))

#dataBulk
#url <- "https://github.com/sistia01/DWLS/raw/main/inst/extdata/dataBulk.RData"
#dest <- "data/dataBulk.RData"
#load(download.file(url, tempfile(dest)))
#load("data/dataBulk.RData")
load(system.file("extdata", "dataBulk.RData", package = "DWLS"))

#labels
#url <- "https://github.com/sistia01/DWLS/raw/main/inst/extdata/labels.RData"
#dest <- "data/labels.RData"
#download.file(url, dest)
#load("data/labels.RData")
load(system.file("extdata", "labels.RData", package = "DWLS"))

#data('trueLabels', package = "DWLS")
#url <- "https://github.com/sistia01/DWLS/raw/main/inst/extdata/trueLabels.RData"
#dest <- "data/trueLabels.RData"
#download.file(url, dest)
#load("data/trueLabels.RData")
load(system.file("extdata", "trueLabels.RData", package = "DWLS"))

pseudo.count = 0.1
data.used.log2 <- log2(dataSC+pseudo.count)
colnames(data.used.log2)<-make.unique(colnames(data.used.log2))
diff.cutoff=0.5
id = labels
for (i in unique(id)){
  cells.symbol.list2 = colnames(data.used.log2)[which(id==i)]
  cells.coord.list2 = match(cells.symbol.list2, colnames(data.used.log2))
  cells.symbol.list1 = colnames(data.used.log2)[which(id != i)]
  cells.coord.list1 = match(cells.symbol.list1, colnames(data.used.log2))
  data.used.log2.ordered = cbind(data.used.log2[,cells.coord.list1],
                                        data.used.log2[,cells.coord.list2])}
group.v <- c(rep(0,length(cells.coord.list1)),
                                         rep(1, length(cells.coord.list2)))

DWLS documentation built on May 24, 2022, 5:07 p.m.