19.1 Exporting fragment-level data
Before we start exporting data, lets save projHeme5 to its own directory.
projHeme5 <- saveArchRProject(ArchRProj = projHeme5, outputDirectory = "Save-ProjHeme5", load = TRUE)
## Copying ArchRProject to new outputDirectory : /corces/home/rcorces/scripts/github/ArchR_Website_Testing/bookdown/Save-ProjHeme5
## Copying Arrow Files...
## Copying Arrow Files (1 of 3)
## Copying Arrow Files (2 of 3)
## Copying Arrow Files (3 of 3)
## Getting ImputeWeights
## Dropping ImputeWeights...
## Copying Other Files...
## Copying Other Files (1 of 11): Annotations
## Copying Other Files (2 of 11): Background-Peaks.rds
## Copying Other Files (3 of 11): Embeddings
## Copying Other Files (4 of 11): GroupCoverages
## Copying Other Files (5 of 11): IterativeLSI
## Copying Other Files (6 of 11): IterativeLSI2
## Copying Other Files (7 of 11): Monocole3
## Copying Other Files (8 of 11): Peak2GeneLinks
## Copying Other Files (9 of 11): PeakCalls
## Copying Other Files (10 of 11): Plots
## Copying Other Files (11 of 11): RNAIntegration
## Saving ArchRProject...
## Loading ArchRProject...
## Successfully loaded ArchRProject!
##
## / |
## / \
## . / |.
## \\\ / |.
## \\\ / `|.
## \\\ / |.
## \ / |\
## \\#####\ / ||
## ==###########> / ||
## \\##==......\ / ||
## ______ = =|__ /__ || \\\
## ,--' ,----`-,__ ___/' --,-`-===================##========>
## \ ' ##_______ _____ ,--,__,=##,__ ///
## , __== ___,-,__,--'#' ===' `-' | ##,-/
## -,____,---' \\####\\________________,--\\_##,/
## ___ .______ ______ __ __ .______
## / \ | _ \ / || | | | | _ \
## / ^ \ | |_) | | ,----'| |__| | | |_) |
## / /_\ \ | / | | | __ | | /
## / _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
## /__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
## To enable optimal flexibility, ArchR allows you to export fragments from your ArchRProject or ArrowFiles at any time using the getFragmentsFromArrow(), getFragmentsFromProject(), and getGroupFragments() functions. For the getFragmentsFromArrow() and getFragmentsFromProject() functions, you must provide the cellNames for the cells you wish to extract. For example, you might extract the fragments from a particular cluster from your entire project like this:
frags <- getFragmentsFromProject(
ArchRProj = projHeme5,
cellNames = getCellNames(ArchRProj = projHeme5)[which(projHeme5@cellColData$Clusters2 == "Mono")]
)
## ArchR logging to : ArchRLogs/ArchR-getFragmentsFromProject-371b0731e4aa7-Date-2022-12-23_Time-09-18-18.log
## If there is an issue, please report to github with logFile!
## Reading ArrowFile 1 of 3
## Reading ArrowFile 2 of 3
## Reading ArrowFile 3 of 3Inspecting the frags object here, shows it to be a list and each of the elements of frags is a GRanges object corresponding to one of the original Arrow Files:
frags
## List of length 3
## names(3): scATAC_BMMC_R1 scATAC_CD34_BMMC_R1 scATAC_PBMC_R1We can just unlist this object to get a GRanges object where each entry represents an individual fragment:
unlist(frags)
## GRanges object with 9487632 ranges and 1 metadata column:
## seqnames ranges strand | RG
## <Rle> <IRanges> <Rle> | <Rle>
## scATAC_BMMC_R1 chr1 713020-713186 * | scATAC_BMMC_R1#CCGTA..
## scATAC_BMMC_R1 chr1 876537-876755 * | scATAC_BMMC_R1#CCGTA..
## scATAC_BMMC_R1 chr1 911371-911637 * | scATAC_BMMC_R1#CCGTA..
## scATAC_BMMC_R1 chr1 954927-954966 * | scATAC_BMMC_R1#CCGTA..
## scATAC_BMMC_R1 chr1 1052090-1052416 * | scATAC_BMMC_R1#CCGTA..
## ... ... ... ... . ...
## scATAC_PBMC_R1 chrY 22737645-22737827 * | scATAC_PBMC_R1#AATGG..
## scATAC_PBMC_R1 chrY 15443307-15443509 * | scATAC_PBMC_R1#GGTGC..
## scATAC_PBMC_R1 chrY 14604751-14604917 * | scATAC_PBMC_R1#CGATG..
## scATAC_PBMC_R1 chrY 5609640-5609780 * | scATAC_PBMC_R1#TATGT..
## scATAC_PBMC_R1 chrY 22737684-22737775 * | scATAC_PBMC_R1#TATGT..
## -------
## seqinfo: 24 sequences from an unspecified genome; no seqlengthsSimilarly, getGroupFragments() provides a shortcut to doing fragment export based on cell groupings defined in cellColData. However, this function creates fragment files on disk, rather than storing them as a GRanges object.
frags <- getGroupFragments(ArchRProj = projHeme5, groupBy = "Clusters2")Inspecting the frags object returned as the output of getGroupFragments(), we get the file paths to the fragment files on disk.
frags
## [1] "/corces/home/rcorces/scripts/github/ArchR_Website_Testing/bookdown/Save-ProjHeme5/GroupFragments/Clusters2.B.tsv.gz"
## [2] "/corces/home/rcorces/scripts/github/ArchR_Website_Testing/bookdown/Save-ProjHeme5/GroupFragments/Clusters2.CD4.M.tsv.gz"
## [3] "/corces/home/rcorces/scripts/github/ArchR_Website_Testing/bookdown/Save-ProjHeme5/GroupFragments/Clusters2.CD4.N.tsv.gz"
## [4] "/corces/home/rcorces/scripts/github/ArchR_Website_Testing/bookdown/Save-ProjHeme5/GroupFragments/Clusters2.CLP.tsv.gz"
## [5] "/corces/home/rcorces/scripts/github/ArchR_Website_Testing/bookdown/Save-ProjHeme5/GroupFragments/Clusters2.Erythroid.tsv.gz"
## [6] "/corces/home/rcorces/scripts/github/ArchR_Website_Testing/bookdown/Save-ProjHeme5/GroupFragments/Clusters2.GMP.tsv.gz"
## [7] "/corces/home/rcorces/scripts/github/ArchR_Website_Testing/bookdown/Save-ProjHeme5/GroupFragments/Clusters2.Mono.tsv.gz"
## [8] "/corces/home/rcorces/scripts/github/ArchR_Website_Testing/bookdown/Save-ProjHeme5/GroupFragments/Clusters2.NK.tsv.gz"
## [9] "/corces/home/rcorces/scripts/github/ArchR_Website_Testing/bookdown/Save-ProjHeme5/GroupFragments/Clusters2.pDC.tsv.gz"
## [10] "/corces/home/rcorces/scripts/github/ArchR_Website_Testing/bookdown/Save-ProjHeme5/GroupFragments/Clusters2.PreB.tsv.gz"
## [11] "/corces/home/rcorces/scripts/github/ArchR_Website_Testing/bookdown/Save-ProjHeme5/GroupFragments/Clusters2.Progenitor.tsv.gz"