# 4.3 实战三 | 10X | 未过滤的PBMC

## 1 前言

相信学习单细胞数据分析的大家对PBMC都不陌生，虽然不是相关背景，但Seurat的PBMC数据深入人心。PBMC全称是peripheral blood mononuclear cell ，外周血单核细胞。

我们这里用的数据集来自[Zheng et al. 2017](https://pubmed.ncbi.nlm.nih.gov/28091601/)，并在[10X Genomics官网也可以获取](https://support.10xgenomics.com/single-cell-gene-expression/datasets/2.1.0/pbmc4k)，数量比Seurat使用的的2700个细胞数据更大

## 2 数据准备

### **下载**

当然也可以跳过这一步，自己下载好之后读入。这里只是学习一下另一种方法

```r
library(BiocFileCache)
bfc <- BiocFileCache("raw_data", ask = FALSE)
raw.path <- bfcrpath(bfc, file.path("http://cf.10xgenomics.com/samples",
    "cell-exp/2.1.0/pbmc4k/pbmc4k_raw_gene_bc_matrices.tar.gz"))
untar(raw.path, exdir=file.path(tempdir(), "pbmc4k"))
# 最后也就是得到这三个文件：barcodes.tsv genes.tsv    matrix.mtx
```

### **读取**

```r
library(DropletUtils)
fname <- file.path(tempdir(), "pbmc4k/raw_gene_bc_matrices/GRCh38")
sce.pbmc <- read10xCounts(fname, col.names=TRUE)
# 看这里的数量惊人，但是后面还需要过滤
sce.pbmc
# class: SingleCellExperiment 
# dim: 33694 737280 
# metadata(1): Samples
# assays(1): counts
# rownames(33694): ENSG00000243485
# ENSG00000237613 ... ENSG00000277475
# ENSG00000268674
# rowData names(2): ID Symbol
# colnames(737280): AAACCTGAGAAACCAT-1
# AAACCTGAGAAACCGC-1 ... TTTGTCATCTTTAGTC-1
# TTTGTCATCTTTCCTC-1
# colData names(2): Sample Barcode
# reducedDimNames(0):
#   altExpNames(0):
```

### **转换ID，添加染色体信息**

```r
library(scater)
rownames(sce.pbmc) <- uniquifyFeatureNames(
    rowData(sce.pbmc)$ID, rowData(sce.pbmc)$Symbol)

library(EnsDb.Hsapiens.v86)
location <- mapIds(EnsDb.Hsapiens.v86, keys=rowData(sce.pbmc)$ID, 
    column="SEQNAME", keytype="GENEID")
```

## 3 质控

10X数据面临的一大问题就是空液滴，因此需要`emptyDrops`检验一下

```r
set.seed(100)
# 对70多万个液滴进行检验
e.out <- emptyDrops(counts(sce.pbmc))
# > e.out
# DataFrame with 737280 rows and 5 columns
# Total   LogProb    PValue   Limited       FDR
# <integer> <numeric> <numeric> <logical> <numeric>
#   AAACCTGAGAAACCAT-1         1        NA        NA        NA        NA
# AAACCTGAGAAACCGC-1         0        NA        NA        NA        NA
# AAACCTGAGAAACCTA-1         1        NA        NA        NA        NA
# AAACCTGAGAAACGAG-1         0        NA        NA        NA        NA
# AAACCTGAGAAACGCC-1         1        NA        NA        NA        NA
# ...                      ...       ...       ...       ...       ...
# TTTGTCATCTTTACAC-1         2        NA        NA        NA        NA
# TTTGTCATCTTTACGT-1        33        NA        NA        NA        NA
# TTTGTCATCTTTAGGG-1         0        NA        NA        NA        NA
# TTTGTCATCTTTAGTC-1         0        NA        NA        NA        NA
# TTTGTCATCTTTCCTC-1         1        NA        NA        NA        NA

# 最后过滤，剩下4000多
sce.pbmc <- sce.pbmc[,which(e.out$FDR <= 0.001)]
sce.pbmc
# class: SingleCellExperiment 
# dim: 33694 4233 
# metadata(1): Samples
# assays(1): counts
# rownames(33694): RP11-34P13.3 FAM138A ...
# AC213203.1 FAM231B
# rowData names(2): ID Symbol
# colnames(4233): AAACCTGAGAAGGCCT-1
# AAACCTGAGACAGACC-1 ... TTTGTCACAGGTCCAC-1
# TTTGTCATCCCAAGAT-1
# colData names(2): Sample Barcode
# reducedDimNames(0):
#   altExpNames(0):
```

### 数据备份

把unfiltered数据主要用在质控的探索上

```r
unfiltered <- sce.pbmc
```

这里过滤的条件不需要太严苛，**只需要去除线粒体含量太高的细胞即可**

> 成熟的mRNA会通过核孔来到细胞质。如果细胞遭到破坏，大量细胞质中mRNA流失，而线粒体体积比较大，流不出去，含量基本不变，最后导致细胞质中捕获的线粒体RNA占比升高

```r
stats <- perCellQCMetrics(sce.pbmc, subsets=list(Mito=which(location=="MT")))
high.mito <- isOutlier(stats$subsets_Mito_percent, type="higher")
sce.pbmc <- sce.pbmc[,!high.mito]

summary(high.mito)
##    Mode   FALSE    TRUE 
## logical    3922     311
```

### **根据原来的数据，加上质控标准作图**

```r
colData(unfiltered) <- cbind(colData(unfiltered), stats)
unfiltered$discard <- high.mito

gridExtra::grid.arrange(
    plotColData(unfiltered, y="sum", colour_by="discard") +
        scale_y_log10() + ggtitle("Total count"),
    plotColData(unfiltered, y="detected", colour_by="discard") +
        scale_y_log10() + ggtitle("Detected features"),
    plotColData(unfiltered, y="subsets_Mito_percent",
        colour_by="discard") + ggtitle("Mito percent"),
    ncol=3
)
```

![](https://jieandze1314-1255603621.cos.ap-guangzhou.myqcloud.com/blog/2020-07-19-100732.png)

### **再看下文库大小分别和线粒体含量的关系**

```r
plotColData(unfiltered, x="sum", y="subsets_Mito_percent",
    colour_by="discard") + scale_x_log10()
```

![](https://jieandze1314-1255603621.cos.ap-guangzhou.myqcloud.com/blog/2020-07-19-100808.png)

## 4 归一化

也是使用预分群+去卷积计算size factor的方法

```r
library(scran)
set.seed(1000)
clusters <- quickCluster(sce.pbmc)
sce.pbmc <- computeSumFactors(sce.pbmc, cluster=clusters)
sce.pbmc <- logNormCounts(sce.pbmc)

summary(sizeFactors(sce.pbmc))
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   0.009   0.710   0.871   1.000   1.094  13.948
```

**看看两种归一化方法的差异**

```r
plot(librarySizeFactors(sce.pbmc), sizeFactors(sce.pbmc), pch=16,
    xlab="Library size factors", ylab="Deconvolution factors", log="xy")
abline(a=0, b=1, col="red")
```

![](https://jieandze1314-1255603621.cos.ap-guangzhou.myqcloud.com/blog/2020-07-19-101041.png)

## 5 找表达量高变化基因

既然有UMI，就可以用第三种方法【在之前 [3.3 挑选高变化基因](https://jieandze1314.osca.top/03/03-3) 的 2.3 考虑技术噪音中介绍过，如果没有spike-in】：可以考虑利用数据分布来表示技术噪音，例如只考虑技术噪音的话，UMI counts通常会呈现近似泊松分布

```r
set.seed(1001)
dec.pbmc <- modelGeneVarByPoisson(sce.pbmc)
top.pbmc <- getTopHVGs(dec.pbmc, prop=0.1)

# 作图
plot(dec.pbmc$mean, dec.pbmc$total, pch=16, cex=0.5,
    xlab="Mean of log-expression", ylab="Variance of log-expression")
curfit <- metadata(dec.pbmc)
# 可视化一条线（下图的蓝线），这条线指所有的基因都会存在的一种偏差
curve(curfit$trend(x), col='dodgerblue', add=TRUE, lwd=2)
```

![](https://jieandze1314-1255603621.cos.ap-guangzhou.myqcloud.com/blog/2020-07-19-101244.png)

## 6 降维

```r
set.seed(10000)
sce.pbmc <- denoisePCA(sce.pbmc, subset.row=top.pbmc, technical=dec.pbmc)

set.seed(100000)
sce.pbmc <- runTSNE(sce.pbmc, dimred="PCA")

set.seed(1000000)
sce.pbmc <- runUMAP(sce.pbmc, dimred="PCA")
```

看看保留了几个PC

```r
ncol(reducedDim(sce.pbmc, "PCA"))
## [1] 8
```

## 7 聚类

```r
g <- buildSNNGraph(sce.pbmc, k=10, use.dimred = 'PCA')
clust <- igraph::cluster_walktrap(g)$membership
colLabels(sce.pbmc) <- factor(clust)

table(colLabels(sce.pbmc))
## 
##   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18 
## 585 518 364 458 170 791 295 107  45  46 152  84  40  60 142  16  28  21

plotTSNE(sce.pbmc, colour_by="label")
```

![](https://jieandze1314-1255603621.cos.ap-guangzhou.myqcloud.com/blog/2020-07-19-101650.png)

## 8 找marker基因并解释结果

```r
markers <- findMarkers(sce.pbmc, pval.type="some", direction="up")
```

这次看看cluster 7的marker基因

```r
marker.set <- markers[["7"]]
as.data.frame(marker.set[1:30,1:3])
# p.value           FDR summary.logFC
# FCN1   4.881588e-137 1.644802e-132      2.715872
# LGALS2 3.729029e-133 6.282295e-129      2.191398
# CSTA   1.426854e-131 1.602548e-127      2.123738
# CFD    1.207067e-102  1.016773e-98      1.503274
# FGL2    8.567117e-93  5.773209e-89      1.358891
# IFI30   7.822561e-80  4.392889e-76      1.276366
# CLEC7A  6.052032e-79  2.913102e-75      1.109366
# MS4A6A  1.958033e-78  8.246744e-75      1.419465
# CFP     8.802407e-73  3.295426e-69      1.312191
# S100A8  6.193215e-70  2.086742e-66      3.431603
```

![](https://jieandze1314-1255603621.cos.ap-guangzhou.myqcloud.com/blog/2020-07-19-102158.png)

再和其他clusters对比

```r
plotExpression(sce.pbmc, features=c("CD14", "CD68",
    "MNDA", "FCGR3A"), x="label", colour_by="label")
```

![](https://jieandze1314-1255603621.cos.ap-guangzhou.myqcloud.com/blog/2020-07-19-102238.png)

其实**最后还是考验的背景知识**：根据cluster7中CD14、CD68、MNDA表达量升高，同时又检查了CD16基因下调，推测cluster7是单核细胞