6.ArchR的可视化（2）：TF activity

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已于 2024-04-23 14:50:29 修改

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分类专栏： ArchR 表观遗传 scATAC-seq 文章标签：聚类 r语言

于 2024-04-23 10:15:32 首次发布

本文链接：https://blog.youkuaiyun.com/jl19930703/article/details/138093346

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本文介绍了ArchR在转录因子活性分析中的可视化方法，包括缺失的Motif序列标识图和时间消耗的讨论。

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> ## 用拿到的确定的（第N版）celltype进行拟混池重复
> library('BSgenome.Hsapiens.UCSC.hg19')
> getCellColData(projHeme2)

> projHeme2 <- addGroupCoverages(ArchRProj=projHeme2, groupBy="celltype") #构建拟混池重复
ArchR logging to : ArchRLogs/ArchR-addGroupCoverages-46462edece89-Date-2024-04-22_Time-21-20-26.log
If there is an issue, please report to github with logFile!
2024-04-22 21:21:09 : Creating Coverage Files!, 0.723 mins elapsed.
2024-04-22 21:21:09 : Batch Execution w/ safelapply!, 0.723 mins elapsed.
2024-04-22 21:25:08 : Adding Kmer Bias to Coverage Files!, 4.705 mins elapsed.
2024-04-22 21:29:29 : Finished Creation of Coverage Files!, 9.057 mins elapsed.
ArchR logging successful to : ArchRLogs/ArchR-addGroupCoverages-46462edece89-Date-2024-04-22_Time-21-20-26.log

> projHeme2 <- addReproduciblePeakSet( #添加可再现峰集
+   ArchRProj = projHeme2, 
+   groupBy="celltype",
+   maxPeaks = 200000,
+   pathToMacs2 = "/home/u37189/miniconda3/envs/Rlibrary/bin/macs2")
ArchR logging to : ArchRLogs/ArchR-addReproduciblePeakSet-46463d5f2b4a-Date-2024-04-22_Time-21-31-10.log
If there is an issue, please report to github with logFile!
2024-04-22 21:31:13 : Peak Calling Parameters!, 0.045 mins elapsed.
                  Group nCells nCellsUsed nReplicates nMin nMax maxPeaks
B cell           B cell   1898       1550           5   81  500   200000
Basophil       Basophil    560        538           4   91  185   200000
CD4M               CD4M   3578       2138           5  194  500   200000
C

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