LinkPeaks with a single gene

[XinWang19]

Hi,
When I performed LinkPeaks with a single gene name like:

LinkPeaks(
object = seurat.obj,
peak.assay = "ATAC",
expression.assay = "RNA",
genes.use = "INS")

It returned:

No peaks fall within distance threshold 
Have you set the proper genome and seqlevelsStyle for ATAC assay?"

I found the problem is caused by line 51 and 57. When genes.use is a single character, the expression.data will become a vector without a row.name.

expression.data <- expression.data[genes.keep, ]
genes <- rownames(x = expression.data)

[timoast]

Thanks for reporting, this should now be fixed on the develop branch. See installation instructions here: https://satijalab.org/signac/articles/install.html#development-version-1