从 edgeR 中的 BCV 图中查找坐标

Question

我如何知道从 edgeR 包生成色散图 (BCV) 的函数 (x) 以及函数的坐标？

我需要知道 "trend" 色散的顶点（每个顶点的最大值和最小值）的 "the coordinates" 以及 "trend line (blue)" 与公共色散线（红线）相交的位置)

为了方便，我做了一个例子：

data <- "chr start end depth depth1 depth2 depth3 depth4 depth5 depth6
chr1 3273 3273 7 200 35 1 200 850 0
chr1 3274 3274 3 50 25 5 300 1500 2
chr1 3275 3275 8 600 15 8 100 300 5
chr1 3276 3276 4 30 2 10 59 20 0
chr1 3277 3277 25 20 7 4 600 45 0"
data <- read.table(text=data, header=T)

datamatrix <- data [, c(4:10)]
library (edgeR)

#grouping factor
group <- c(1, 2, 2, 2, 2, 2, 2) #groups of each sample)

#create a DGEList
y <- DGEList(counts=datamatrix,group=group)

根据 edgeR 包，我可以使用以下方法估计数据集的分散度：

y <- estimateDisp(y) 

y$common.dispersion

共同色散的平方根给出生物变异系数。并且，可以在 BCV 图中查看离散估计：

plotBCV(y)

Answer 1

我认为这解决了问题

#finding dispersion coordinates

    afun <- approxfun(y$AveLogCPM, y$trended.dispersion)

#ranging between -2 and 12 the "par" number to check the intersection
    optim(par=-1, function(x) { (afun(x) - y$common.dispersion)^2 }) #-0.9056
    optim(par=0, function(x) { (afun(x) - y$common.dispersion)^2 }) #-0.4955
    optim(par=2, function(x) { (afun(x) - y$common.dispersion)^2 }) #1.8237

#with the plotBCV function code, I have the access to tagwise, trended, common dispersions, and the abundance values, for each CpG as: y$tagwise.dispersion, y$trended.dispersion, y$common.dispersion, and y$AveLogCPM, respectively. 

min (y$trended.dispersion) #[1] 1.09009
max (y$trended.dispersion) #[1] 1.50691

#to the vertex, you can subset a table according to the AveLogCPM range that you want to know the max and min like this:

afuntable<- data.table(y$AveLogCPM, y$trended.dispersion)
afuntablemod <-subset (afuntable, V1 >= 0)
afuntablemod <-subset (afuntablemod, V1 <= 2)
min (afuntablemod$V2) #[1] 1.318002

#and again
afuntable<- data.table(y$AveLogCPM, y$trended.dispersion)
afuntablemod <-subset (afuntable, V1 >= 2)
afuntablemod <-subset (afuntablemod, V1 <= 12)
max (afuntablemod$V2) #[1] 1.50691

从 edgeR 中的 BCV 图中查找坐标

Finding the coordinates from a BCV plot in edgeR

r

function

math

coordinates

bioconductor