## 9.2 Making Pseudo-bulk Replicates

In ArchR, pseudo-bulk replicates are made using the `addGroupCoverages()`

function. The key parameter here is `groupBy`

which defines the groups for which pseudo-bulk replicates should be made. Here, we are using `Clusters2`

which was defined by labeling our clusters with cell types defined by scRNA-seq data in a previous chapter.

## ArchR logging to : ArchRLogs/ArchR-addGroupCoverages-faba40cd6ba1-Date-2020-04-15_Time-10-23-14.log

## If there is an issue, please report to github with logFile!

## B CellGroups N = 2CD4.M CellGroups N = 2CD4.N CellGroups N = 2CLP CellGroups N = 2Erythroid CellGroups N = 2GMP CellGroups N = 2Mono CellGroups N = 2NK CellGroups N = 2pDC CellGroups N = 2PreB CellGroups N = 2Progenitor CellGroups N = 2

## B CellGroups N = 2CD4.M CellGroups N = 2CD4.N CellGroups N = 2CLP CellGroups N = 2Erythroid CellGroups N = 2GMP CellGroups N = 2Mono CellGroups N = 2NK CellGroups N = 2pDC CellGroups N = 2PreB CellGroups N = 2Progenitor CellGroups N = 2

## B CellGroups N = 2CD4.M CellGroups N = 2CD4.N CellGroups N = 2CLP CellGroups N = 2Erythroid CellGroups N = 2GMP CellGroups N = 2Mono CellGroups N = 2NK CellGroups N = 2pDC CellGroups N = 2PreB CellGroups N = 2Progenitor CellGroups N = 2

## B CellGroups N = 2CD4.M CellGroups N = 2CD4.N CellGroups N = 2CLP CellGroups N = 2Erythroid CellGroups N = 2GMP CellGroups N = 2Mono CellGroups N = 2NK CellGroups N = 2pDC CellGroups N = 2PreB CellGroups N = 2Progenitor CellGroups N = 2

## B CellGroups N = 2CD4.M CellGroups N = 2CD4.N CellGroups N = 2CLP CellGroups N = 2Erythroid CellGroups N = 2GMP CellGroups N = 2Mono CellGroups N = 2NK CellGroups N = 2pDC CellGroups N = 2PreB CellGroups N = 2Progenitor CellGroups N = 2

## B CellGroups N = 2CD4.M CellGroups N = 2CD4.N CellGroups N = 2CLP CellGroups N = 2Erythroid CellGroups N = 2GMP CellGroups N = 2Mono CellGroups N = 2NK CellGroups N = 2pDC CellGroups N = 2PreB CellGroups N = 2Progenitor CellGroups N = 2

## B CellGroups N = 2CD4.M CellGroups N = 2CD4.N CellGroups N = 2CLP CellGroups N = 2Erythroid CellGroups N = 2GMP CellGroups N = 2Mono CellGroups N = 2NK CellGroups N = 2pDC CellGroups N = 2PreB CellGroups N = 2Progenitor CellGroups N = 2

## B CellGroups N = 2CD4.M CellGroups N = 2CD4.N CellGroups N = 2CLP CellGroups N = 2Erythroid CellGroups N = 2GMP CellGroups N = 2Mono CellGroups N = 2NK CellGroups N = 2pDC CellGroups N = 2PreB CellGroups N = 2Progenitor CellGroups N = 2

## B CellGroups N = 2CD4.M CellGroups N = 2CD4.N CellGroups N = 2CLP CellGroups N = 2Erythroid CellGroups N = 2GMP CellGroups N = 2Mono CellGroups N = 2NK CellGroups N = 2pDC CellGroups N = 2PreB CellGroups N = 2Progenitor CellGroups N = 2

## B CellGroups N = 2CD4.M CellGroups N = 2CD4.N CellGroups N = 2CLP CellGroups N = 2Erythroid CellGroups N = 2GMP CellGroups N = 2Mono CellGroups N = 2NK CellGroups N = 2pDC CellGroups N = 2PreB CellGroups N = 2Progenitor CellGroups N = 2

## B CellGroups N = 2CD4.M CellGroups N = 2CD4.N CellGroups N = 2CLP CellGroups N = 2Erythroid CellGroups N = 2GMP CellGroups N = 2Mono CellGroups N = 2NK CellGroups N = 2pDC CellGroups N = 2PreB CellGroups N = 2Progenitor CellGroups N = 2

## 2020-04-15 10:23:17 : Creating Coverage Files!, 0.046 mins elapsed.

## 2020-04-15 10:23:17 : Batch Execution w/ safelapply!, 0.046 mins elapsed.

## 2020-04-15 10:24:14 : Adding Kmer Bias to Coverage Files!, 0.996 mins elapsed.

##

## Completed Kmer Bias Calculation

## Adding Kmer Bias (1 of 22)

## Adding Kmer Bias (2 of 22)

## Adding Kmer Bias (3 of 22)

## Adding Kmer Bias (4 of 22)

## Adding Kmer Bias (5 of 22)

## Adding Kmer Bias (6 of 22)

## Adding Kmer Bias (7 of 22)

## Adding Kmer Bias (8 of 22)

## Adding Kmer Bias (9 of 22)

## Adding Kmer Bias (10 of 22)

## Adding Kmer Bias (11 of 22)

## Adding Kmer Bias (12 of 22)

## Adding Kmer Bias (13 of 22)

## Adding Kmer Bias (14 of 22)

## Adding Kmer Bias (15 of 22)

## Adding Kmer Bias (16 of 22)

## Adding Kmer Bias (17 of 22)

## Adding Kmer Bias (18 of 22)

## Adding Kmer Bias (19 of 22)

## Adding Kmer Bias (20 of 22)

## Adding Kmer Bias (21 of 22)

## Adding Kmer Bias (22 of 22)

## 2020-04-15 10:25:16 : Finished Creation of Coverage Files!, 2.022 mins elapsed.

## ArchR logging successful to : ArchRLogs/ArchR-addGroupCoverages-faba40cd6ba1-Date-2020-04-15_Time-10-23-14.log

With these pseudo-bulk replicates generated, we can now call peaks in our data. As mentioned previously, we do not want to call peaks on the merged set of all single cells so having these more granular cell groups defined, either through clustering or otherwise, provides the ideal starting point for peak calling.