16.3 Feature Footprinting

In addition to footprinting motifs, ArchR enables footprinting of any user-defined feature set. To illustrate this capability, we will use the plotFootprints() function to create a TSS insertion profile (introduced previously during the section on data quality control). A TSS insertion profile is just a specialized sub-case of footprinting.

As discussed in the previous section, footprinting is performed using group coverage files which are derived from pseudo-bulk replicates. We originally created these in a previous chapter to perform peak calling. If you haven’t already added group coverages to your ArchRProject, lets do that now.

if(is.null(projHeme5@projectMetadata$GroupCoverages$Clusters2)){
  projHeme5 <- addGroupCoverages(ArchRProj = projHeme5, groupBy = "Clusters2")
}

We create TSS insertion profiles without normalization for Tn5 bias. The main difference from our previous analyses is that we specify flank = 2000 to extend these footprints 2000 bp on either side of each TSS.

seTSS <- getFootprints(
  ArchRProj = projHeme5, 
  positions = GRangesList(TSS = getTSS(projHeme5)), 
  groupBy = "Clusters2",
  flank = 2000
)
## ArchR logging to : ArchRLogs/ArchR-getFootprints-371b08eddf1a-Date-2022-12-23_Time-08-37-04.log
## If there is an issue, please report to github with logFile!
## 2022-12-23 08:37:05 : Computing Kmer Bias Table, 0.02 mins elapsed.
## 2022-12-23 08:37:21 : Finished Computing Kmer Tables, 0.274 mins elapsed.
## 2022-12-23 08:37:21 : Computing Footprints, 0.294 mins elapsed.
## 2022-12-23 08:37:36 : Computing Footprints Bias, 0.542 mins elapsed.
## 2022-12-23 08:37:51 : Summarizing Footprints, 0.785 mins elapsed.

We can then plot the TSS insertion profiles for each cell group using plotFootprints().

plotFootprints(
  seFoot = seTSS,
  ArchRProj = projHeme5, 
  normMethod = "None",
  plotName = "TSS-No-Normalization",
  addDOC = FALSE,
  flank = 2000,
  flankNorm = 100
)
## ArchR logging to : ArchRLogs/ArchR-plotFootprints-371b0f82c713-Date-2022-12-23_Time-08-37-53.log
## If there is an issue, please report to github with logFile!
## 2022-12-23 08:37:54 : Plotting Footprint : TSS (1 of 1), 0.019 mins elapsed.
## Normalizing by flanking regions
## NormMethod = None
## ArchR logging successful to : ArchRLogs/ArchR-plotFootprints-371b0f82c713-Date-2022-12-23_Time-08-37-53.log