Procedure:
# Summary of ATAC-seq peaks
proj<-loadArchRProject("all_sample_DA/")
proj@peakSet@metadata$PeakCallSummary[1:4,]
Group | Var1 | Freq | |
---|---|---|---|
<chr> | <fct> | <dbl> | |
1 | UnionPeaks | Distal | 29.672 |
2 | UnionPeaks | Exonic | 12.096 |
3 | UnionPeaks | Intronic | 59.553 |
4 | UnionPeaks | Promoter | 19.355 |
The heatmap rows are clustered by k-means clustering based on k=25. The side-by-side heatmap of linked ATAC (left) and gene regions (right) shows the correspondence of peak-to-gene links between two dataset.
p
ArchR logging to : ArchRLogs/ArchR-peakAnnoEnrichment-ad1329967bfe-Date-2024-05-25_Time-15-48-27.log If there is an issue, please report to github with logFile! 2024-05-25 15:48:32 : Computing Enrichments 1 of 1, 0.082 mins elapsed. ArchR logging successful to : ArchRLogs/ArchR-peakAnnoEnrichment-ad1329967bfe-Date-2024-05-25_Time-15-48-27.log Warning message: “ggrepel: 39 unlabeled data points (too many overlaps). Consider increasing max.overlaps”
ArchR logging to : ArchRLogs/ArchR-peakAnnoEnrichment-ad13729b439e-Date-2024-05-25_Time-15-20-42.log If there is an issue, please report to github with logFile! 2024-05-25 15:20:47 : Computing Enrichments 1 of 1, 0.08 mins elapsed. ArchR logging successful to : ArchRLogs/ArchR-peakAnnoEnrichment-ad13729b439e-Date-2024-05-25_Time-15-20-42.log Warning message: “ggrepel: 39 unlabeled data points (too many overlaps). Consider increasing max.overlaps”
ArchR logging to : ArchRLogs/ArchR-peakAnnoEnrichment-ad1311fe8433-Date-2024-05-25_Time-15-49-02.log If there is an issue, please report to github with logFile! 2024-05-25 15:49:07 : Computing Enrichments 1 of 1, 0.083 mins elapsed. ArchR logging successful to : ArchRLogs/ArchR-peakAnnoEnrichment-ad1311fe8433-Date-2024-05-25_Time-15-49-02.log Warning message: “ggrepel: 40 unlabeled data points (too many overlaps). Consider increasing max.overlaps”
ArchR logging to : ArchRLogs/ArchR-peakAnnoEnrichment-ad13533ada3c-Date-2024-05-25_Time-15-51-04.log If there is an issue, please report to github with logFile! 2024-05-25 15:51:09 : Computing Enrichments 1 of 1, 0.083 mins elapsed. ArchR logging successful to : ArchRLogs/ArchR-peakAnnoEnrichment-ad13533ada3c-Date-2024-05-25_Time-15-51-04.log Warning message: “ggrepel: 40 unlabeled data points (too many overlaps). Consider increasing max.overlaps”
ArchR logging to : ArchRLogs/ArchR-peakAnnoEnrichment-ad13559d53e6-Date-2024-05-25_Time-16-01-52.log If there is an issue, please report to github with logFile! 2024-05-25 16:01:56 : Computing Enrichments 1 of 1, 0.08 mins elapsed. ArchR logging successful to : ArchRLogs/ArchR-peakAnnoEnrichment-ad13559d53e6-Date-2024-05-25_Time-16-01-52.log Warning message: “ggrepel: 40 unlabeled data points (too many overlaps). Consider increasing max.overlaps”
ArchR logging to : ArchRLogs/ArchR-peakAnnoEnrichment-ad13313c7218-Date-2024-05-25_Time-16-01-58.log If there is an issue, please report to github with logFile! 2024-05-25 16:02:03 : Computing Enrichments 1 of 1, 0.077 mins elapsed. ArchR logging successful to : ArchRLogs/ArchR-peakAnnoEnrichment-ad13313c7218-Date-2024-05-25_Time-16-01-58.log Warning message: “ggrepel: 35 unlabeled data points (too many overlaps). Consider increasing max.overlaps”