6.ArchR的可视化（5）：共可及性co-accessibility

最新推荐文章于 2024-09-12 18:07:52 发布

武艺晴小朋友你好

最新推荐文章于 2024-09-12 18:07:52 发布

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

本文链接：https://blog.csdn.net/jl19930703/article/details/138168260

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本文介绍了使用ArchR在R语言环境中进行共可及性co-accessibility的可视化，重点关注了peak to peak的共开放情况，并通过浏览器轨迹图展示了结果。此外，还提及了如何鉴定正向调控因子，特别是针对健康骨髓中B细胞系的正向调控转录因子的步骤。

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1) peak to peak
>########################## B细胞系中的共可及性#######################################
> #addCoAccessibility()函数计算共开放性
> projHeme2 <- addCoAccessibility(
                    ArchRProj = projHeme2,
                    reducedDims = "PeakMatrix-IterativeLSI")
ArchR logging to : ArchRLogs/ArchR-addCoAccessibility-17d11988fcb4-Date-2024-04-24_Time-19-46-12.log
If there is an issue, please report to github with logFile!
2024-04-24 19:46:42 : Computing KNN, 0.509 mins elapsed.
2024-04-24 19:47:43 : Identifying Non-Overlapping KNN pairs, 1.529 mins elapsed.
2024-04-24 19:47:46 : Identified 500 Groupings!, 1.581 mins elapsed.
2024-04-24 19:48:14 : Computing Co-Accessibility chr1 (1 of 23), 2.04 mins elapsed.
2024-04-24 19:48:46 : Computing Co-Accessibility chr2 (2 of 23), 2.58 mins elapsed.
2024-04-24 19:49:14 : Computing Co-Accessibility chr3 (3 of 23), 3.035 mins elapsed.
2024-04-24 19:49:35 : Computing Co-Accessibility chr4 (4 of 23), 3.386 mins elapsed.
2024-04-24 19:49:51 : Computing Co-Accessibility chr5 (5 of 23), 3.653 mins elapsed.
2024-04-24 19:50:11 : Computing Co-Accessibility chr6 (6 of 23), 3.994 mins elapsed.
2024-04-24 19:50:33 : Computing Co-Accessibility chr7 (7 of 23), 4.361 mins elapsed.
2024-04-24 19:50:53 : Computing Co-Accessibility chr8 (8 of 23), 4.684 mins elapsed.
2024-04-24 19:51:15 : Computing Co-Accessibility chr9 (9 of 23), 5.063 mins elapsed.
2024-04-24 19:51:33 : Computing Co-Accessibility chr10 (10 of 23), 5.363 mins elapsed.
2024-04-24 19:51:50 : Computing Co-Accessibility chr11 (11 of 23), 5.643 mins elapsed.
2024-04-24 19:52:07 : Computing Co-Accessibility chr12 (12 of 23), 5.923 mins elapsed.
2024-04-24 19:52:23 : Computing Co-Accessibility chr13 (13 of 23), 6.185 mins elapsed.
2024-04-24 19:52:32 : Computing Co-Accessibility chr14 (14 of 23), 6.347 mins elapsed.
2024-04-24 19:52:45 : Computing Co-Accessibility chr15 (15 of 23), 6.555 mins elapsed.
2024-04-24 19:52:56 : Computing Co-Accessibility chr16 (16 of 23), 6.747 mins elapsed.
2024-04-24 19:53:10 : Computing Co-Accessibility chr17 (17 of 23), 6.978 mins elapsed.
2024-04-24 19:53:27 : Computing Co-Accessibility chr18 (18 of 23), 7.253 mins elapsed.
2024-04-24 19:53:38 : Computing Co-Accessibility chr19 (19 of 23), 7.432 mins elapsed.
2024-04-24 19:53:56 : Computing Co-Accessibility chr20 (20 of 23), 7.735 mins elapsed.
2024-04-24 19:54:07 : Computing Co-Accessibility chr21 (21 of 23), 7.924 mins elapsed.
2024-04-24 19:54:15 : Computing