stat.log2 {DWLS}

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)))