19.4 Exporting pseudo-bulked data to a bigWig file

Another common use for pseudo-bulked data is to look at genome browser tracks. Of course, ArchR does have its own built-in genome browser which can be accessed via ArchRBrowser(), but we also enable users to export pseudo-bulked bigWig tracks for use with other tools. To do this, we use the getGroupBW() function. This function uses the same groupBy parameter as above. Additionally, users can toggle how the tracks are normalized but we recommend the default which is “ReadsInTSS” which simultaneously normalized for sequencing depth and data quality.

When we run this function, a folder is created within the outputDirectory of our ArchRProject called “GroupBigWigs” and within that directory a subdirectory is created based on the value passed to groupBy. In the below example, we extract bigWig tracks for each group in Clusters2:

coverageFiles <- getGroupBW(ArchRProj = projHeme5, groupBy = "Clusters2")
## ArchR logging to : ArchRLogs/ArchR-getGroupBW-371b024857b00-Date-2022-12-23_Time-09-19-56.log
## If there is an issue, please report to github with logFile!
## 2022-12-23 09:20:04 : B (1 of 11) : Creating BigWig for Group, 0.128 mins elapsed.
## 2022-12-23 09:20:23 : CD4.M (2 of 11) : Creating BigWig for Group, 0.442 mins elapsed.
## 2022-12-23 09:20:38 : CD4.N (3 of 11) : Creating BigWig for Group, 0.701 mins elapsed.
## 2022-12-23 09:20:54 : CLP (4 of 11) : Creating BigWig for Group, 0.964 mins elapsed.
## 2022-12-23 09:21:09 : Erythroid (5 of 11) : Creating BigWig for Group, 1.205 mins elapsed.
## 2022-12-23 09:21:25 : GMP (6 of 11) : Creating BigWig for Group, 1.475 mins elapsed.
## 2022-12-23 09:21:46 : Mono (7 of 11) : Creating BigWig for Group, 1.818 mins elapsed.
## 2022-12-23 09:22:05 : NK (8 of 11) : Creating BigWig for Group, 2.151 mins elapsed.
## 2022-12-23 09:22:22 : pDC (9 of 11) : Creating BigWig for Group, 2.428 mins elapsed.
## 2022-12-23 09:22:40 : PreB (10 of 11) : Creating BigWig for Group, 2.729 mins elapsed.
## 2022-12-23 09:22:52 : Progenitor (11 of 11) : Creating BigWig for Group, 2.921 mins elapsed.
## ArchR logging successful to : ArchRLogs/ArchR-getGroupBW-371b024857b00-Date-2022-12-23_Time-09-19-56.log

The return value of getGroupBW() is a vector of file paths to the created bigWig files.

coverageFiles
##  [1] "/corces/home/rcorces/scripts/github/ArchR_Website_Testing/bookdown/Save-ProjHeme5/GroupBigWigs/Clusters2/B-TileSize-100-normMethod-ReadsInTSS-ArchR.bw"         
##  [2] "/corces/home/rcorces/scripts/github/ArchR_Website_Testing/bookdown/Save-ProjHeme5/GroupBigWigs/Clusters2/CD4.M-TileSize-100-normMethod-ReadsInTSS-ArchR.bw"     
##  [3] "/corces/home/rcorces/scripts/github/ArchR_Website_Testing/bookdown/Save-ProjHeme5/GroupBigWigs/Clusters2/CD4.N-TileSize-100-normMethod-ReadsInTSS-ArchR.bw"     
##  [4] "/corces/home/rcorces/scripts/github/ArchR_Website_Testing/bookdown/Save-ProjHeme5/GroupBigWigs/Clusters2/CLP-TileSize-100-normMethod-ReadsInTSS-ArchR.bw"       
##  [5] "/corces/home/rcorces/scripts/github/ArchR_Website_Testing/bookdown/Save-ProjHeme5/GroupBigWigs/Clusters2/Erythroid-TileSize-100-normMethod-ReadsInTSS-ArchR.bw" 
##  [6] "/corces/home/rcorces/scripts/github/ArchR_Website_Testing/bookdown/Save-ProjHeme5/GroupBigWigs/Clusters2/GMP-TileSize-100-normMethod-ReadsInTSS-ArchR.bw"       
##  [7] "/corces/home/rcorces/scripts/github/ArchR_Website_Testing/bookdown/Save-ProjHeme5/GroupBigWigs/Clusters2/Mono-TileSize-100-normMethod-ReadsInTSS-ArchR.bw"      
##  [8] "/corces/home/rcorces/scripts/github/ArchR_Website_Testing/bookdown/Save-ProjHeme5/GroupBigWigs/Clusters2/NK-TileSize-100-normMethod-ReadsInTSS-ArchR.bw"        
##  [9] "/corces/home/rcorces/scripts/github/ArchR_Website_Testing/bookdown/Save-ProjHeme5/GroupBigWigs/Clusters2/pDC-TileSize-100-normMethod-ReadsInTSS-ArchR.bw"       
## [10] "/corces/home/rcorces/scripts/github/ArchR_Website_Testing/bookdown/Save-ProjHeme5/GroupBigWigs/Clusters2/PreB-TileSize-100-normMethod-ReadsInTSS-ArchR.bw"      
## [11] "/corces/home/rcorces/scripts/github/ArchR_Website_Testing/bookdown/Save-ProjHeme5/GroupBigWigs/Clusters2/Progenitor-TileSize-100-normMethod-ReadsInTSS-ArchR.bw"