Bug: get_anchor_stats() requiring `sds` when not `protein` specified

[mgrout81]

I'm running get_anchor_stats() from v1.2.2 of InSituType, Built: R 4.3.1; x86_64-pc-linux-gnu; 2023-12-21 08:16:52 UTC; unix .

The function is asking me for an sds object, but the documentation says sds is only for assay_type = "protein".

> astats_old <- get_anchor_stats(counts = counts,
+                                neg = neg_means,
+                                profiles = oldprofiles)
The following genes in the count data are missing from fixed_profiles and will be omitted from downstream: CCL15,CCL18,CCL23,CCL3,CCL3L3,CCL4,CCL4L2,CCL5,CD24,CYTOR,FCGBP,FYB1,GDF10,H2AZ1,H4C3,LINC02446,MMP12,MRC1,MSMB,PECAM1,PRSS2,SELENOP,VEGFD,VSIR
Error in get_anchor_stats(counts = counts, neg = neg_means, profiles = oldprofiles) : 
  argument "sds" is missing, with no default
> astats_old <- get_anchor_stats(counts = counts,
+                                neg = neg_means,
+                                profiles = oldprofiles, assay_type = "rna")
The following genes in the count data are missing from fixed_profiles and will be omitted from downstream: CCL15,CCL18,CCL23,CCL3,CCL3L3,CCL4,CCL4L2,CCL5,CD24,CYTOR,FCGBP,FYB1,GDF10,H2AZ1,H4C3,LINC02446,MMP12,MRC1,MSMB,PECAM1,PRSS2,SELENOP,VEGFD,VSIR
Error in get_anchor_stats(counts = counts, neg = neg_means, profiles = oldprofiles,  : 
  argument "sds" is missing, with no default
>

Running with sds = NULL appears to help. Above errors printed almost immediately, while with sds = NULL has had the function running for several minutes with no errors yet.

[github-actions[bot]]

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Thanks, NanoString Dev Team

[patrickjdanaher]

fixed in upcoming 2.0 release