Extracting motif matches matrix with genomic coordinates

[fwim]

Dear ArchR Team,

I started using ArchR a couple of months back for a large scATAC-seq experiment and I am so excited about how well it runs on a standard macbook pro.

Now, I am trying to extract a motif matches matrix (TF motifs as cols, peaks as row, cells with binary data t/f for presence/absence of TF binding motif in peak) for downstream analysis. I used “getMatches()” but there is no information on the peak coordinates (chr, start, end) in the row annotations or row names of the object returned by the function.

Do you know whether there is a way to retrieve a motif matches matrix that contains the genomic coordinates of the peaks?

Many thanks,
Florian

[rcorces]

The peak order in the return of getMatches() is the same as the peak order from getPeakSet().
I have updated the function description via 18bcead

[fwim]

Many thanks! That solved the issue.